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Zhou X, Kong X, Lu J, Wang H, Liu M, Zhao S, Xia Z, Liu Q, Sun H, Gao X, Ma C, Niu Z, Yang F, Song X, Gao H, Zhang S, Zhu H. Circulating tumor cell-derived exosome-transmitted long non-coding RNA TTN-AS1 can promote the proliferation and migration of cholangiocarcinoma cells. J Nanobiotechnology 2024; 22:191. [PMID: 38637832 PMCID: PMC11025154 DOI: 10.1186/s12951-024-02459-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 04/04/2024] [Indexed: 04/20/2024] Open
Abstract
BACKGROUND Exosomes assume a pivotal role as essential mediators of intercellular communication within tumor microenvironments. Within this context, long noncoding RNAs (LncRNAs) have been observed to be preferentially sorted into exosomes, thus exerting regulatory control over the initiation and progression of cancer through diverse mechanisms. RESULTS Exosomes were successfully isolated from cholangiocarcinoma (CCA) CTCs organoid and healthy human serum. Notably, the LncRNA titin-antisense RNA1 (TTN-AS1) exhibited a conspicuous up-regulation within CCA CTCs organoid derived exosomes. Furthermore, a significant elevation of TTN-AS1 expression was observed in tumor tissues, as well as in blood and serum exosomes from patients afflicted with CCA. Importantly, this hightened TTN-AS1 expression in serum exosomes of CCA patients manifested a strong correlation with both lymph node metastasis and TNM staging. Remarkably, both CCA CTCs organoid-derived exosomes and CCA cells-derived exosomes featuring pronounced TTN-AS1 expression demonstrated the capability to the proliferation and migratory potential of CCA cells. Validation of these outcomes was conducted in vivo experiments. CONCLUSIONS In conclusion, our study elucidating that CCA CTCs-derived exosomes possess the capacity to bolster the metastasis tendencies of CCA cells by transporting TTN-AS1. These observations underscore the potential of TTN-AS1 within CTCs-derived exosomes to serve as a promising biomarker for the diagnosis and therapeutic management of CCA.
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Affiliation(s)
- Xu Zhou
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, No. 324, Jingwu Road, Jinan, Shandong, 250021, China
- Department of Hepatobiliary Surgery, Cheeloo College of Medicine, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
| | - Xiaohan Kong
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, No. 324, Jingwu Road, Jinan, Shandong, 250021, China
| | - Jun Lu
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, No. 324, Jingwu Road, Jinan, Shandong, 250021, China
- Department of Hepatobiliary Surgery, Cheeloo College of Medicine, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
| | - Heng Wang
- Department of Hepatobiliary Surgery, Cheeloo College of Medicine, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
| | - Meng Liu
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, No. 324, Jingwu Road, Jinan, Shandong, 250021, China
| | - Shuchao Zhao
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, No. 324, Jingwu Road, Jinan, Shandong, 250021, China
| | - Zhaozhi Xia
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, No. 324, Jingwu Road, Jinan, Shandong, 250021, China
| | - Qinggong Liu
- Department of Hepatobiliary Surgery, Cheeloo College of Medicine, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
| | - Hongrui Sun
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, No. 324, Jingwu Road, Jinan, Shandong, 250021, China
| | - Xin Gao
- Department of Hepatobiliary Surgery, Cheeloo College of Medicine, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
| | - Chaoqun Ma
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, No. 324, Jingwu Road, Jinan, Shandong, 250021, China
- Department of Hepatobiliary Surgery, Cheeloo College of Medicine, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
| | - Zheyu Niu
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, No. 324, Jingwu Road, Jinan, Shandong, 250021, China
- Department of Hepatobiliary Surgery, Cheeloo College of Medicine, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
| | - Faji Yang
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, No. 324, Jingwu Road, Jinan, Shandong, 250021, China
- Department of Hepatobiliary Surgery, Cheeloo College of Medicine, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
| | - Xie Song
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, No. 324, Jingwu Road, Jinan, Shandong, 250021, China
- Department of Hepatobiliary Surgery, Cheeloo College of Medicine, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
| | - Hengjun Gao
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, No. 324, Jingwu Road, Jinan, Shandong, 250021, China
- Department of Hepatobiliary Surgery, Cheeloo College of Medicine, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
| | - Shizhe Zhang
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, No. 324, Jingwu Road, Jinan, Shandong, 250021, China
- Department of Hepatobiliary Surgery, Cheeloo College of Medicine, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
| | - Huaqiang Zhu
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, No. 324, Jingwu Road, Jinan, Shandong, 250021, China.
- Department of Hepatobiliary Surgery, Cheeloo College of Medicine, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China.
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Khatik SY, Roy S, Srivatsan SG. Synthesis and Enzymatic Incorporation of a Dual-App Nucleotide Probe That Reports Antibiotics-Induced Conformational Change in the Bacterial Ribosomal Decoding Site RNA. ACS Chem Biol 2024; 19:687-695. [PMID: 38407057 DOI: 10.1021/acschembio.3c00676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Natural nucleosides are nonfluorescent and do not have intrinsic labels that can be readily utilized for analyzing nucleic acid structure and recognition. In this regard, researchers typically use the so-called "one-label, one-technique" approach to study nucleic acids. However, we envisioned that a responsive dual-app nucleoside system that harnesses the power of two complementing biophysical techniques namely, fluorescence and 19F NMR, will allow the investigation of nucleic acid conformations more comprehensively than before. We recently introduced a nucleoside analogue by tagging trifluoromethyl-benzofuran at the C5 position of 2'-deoxyuridine, which serves as an excellent fluorescent and 19F NMR probe to study G-quadruplex and i-motif structures. Taking forward, here, we report the development of a ribonucleotide version of the dual-app probe to monitor antibiotics-induced conformational changes in RNA. The ribonucleotide analog is derived by conjugating trifluoromethyl-benzofuran at the C5 position of uridine (TFBF-UTP). The analog is efficiently incorporated by T7 RNA polymerase to produce functionalized RNA transcripts. Detailed photophysical and 19F NMR of the nucleoside and nucleotide incorporated into RNA oligonucleotides revealed that the analog is structurally minimally invasive and can be used for probing RNA conformations by fluorescence and 19F NMR techniques. Using the probe, we monitored and estimated aminoglycoside antibiotics binding to the bacterial ribosomal decoding site RNA (A-site, a very important RNA target). While 2-aminopurine, a famous fluorescent nucleic acid probe, fails to detect structurally similar aminoglycoside antibiotics binding to the A-site, our probe reports the binding of different aminoglycosides to the A-site. Taken together, our results demonstrate that TFBF-UTP is a very useful addition to the nucleic acid analysis toolbox and could be used to devise discovery platforms to identify new RNA binders of therapeutic potential.
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Affiliation(s)
- Saddam Y Khatik
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
| | - Sarupa Roy
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
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Krohmaly KI, Perez-Losada M, Ramos-Tapia I, Zhu Z, Hasegawa K, Camargo Jr. CA, Harmon B, Espinola JA, Reck Cechinel L, Batabyal R, Freishtat RJ, Hahn A. Bacterial small RNAs may mediate immune response differences seen in respiratory syncytial virus versus rhinovirus bronchiolitis. Front Immunol 2024; 15:1330991. [PMID: 38410509 PMCID: PMC10895043 DOI: 10.3389/fimmu.2024.1330991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 01/24/2024] [Indexed: 02/28/2024] Open
Abstract
Bronchiolitis, a viral lower respiratory infection, is the leading cause of infant hospitalization, which is associated with an increased risk for developing asthma later in life. Bronchiolitis can be caused by several respiratory viruses, such as respiratory syncytial virus (RSV), rhinovirus (RV), and others. It can also be caused by a solo infection (e.g., RSV- or RV-only bronchiolitis) or co-infection with two or more viruses. Studies have shown viral etiology-related differences between RSV- and RV-only bronchiolitis in the immune response, human microRNA (miRNA) profiles, and dominance of certain airway microbiome constituents. Here, we identified bacterial small RNAs (sRNAs), the prokaryotic equivalent to eukaryotic miRNAs, that differ between infants of the 35th Multicenter Airway Research Collaboration (MARC-35) cohort with RSV- versus RV-only bronchiolitis. We first derived reference sRNA datasets from cultures of four bacteria known to be associated with bronchiolitis (i.e., Haemophilus influenzae, Moraxella catarrhalis, Moraxella nonliquefaciens, and Streptococcus pneumoniae). Using these reference sRNA datasets, we found several sRNAs associated with RSV- and RV-only bronchiolitis in our human nasal RNA-Seq MARC-35 data. We also determined potential human transcript targets of the bacterial sRNAs and compared expression of the sRNAs between RSV- and RV-only cases. sRNAs are known to downregulate their mRNA target, we found that, compared to those associated with RV-only bronchiolitis, sRNAs associated with RSV-only bronchiolitis may relatively activate the IL-6 and IL-8 pathways and relatively inhibit the IL-17A pathway. These data support that bacteria may be contributing to inflammation differences seen in RSV- and RV-only bronchiolitis, and for the first time indicate that the potential mechanism in doing so may be through bacterial sRNAs.
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Affiliation(s)
- Kylie I. Krohmaly
- Integrated Biomedical Sciences, The George Washington University, Washington, DC, United States
- Center for Genetic Medicine Research, Children’s National Research and Innovation Center, Washington, DC, United States
| | - Marcos Perez-Losada
- Department of Biostatistics and Bioinformatics, Computational Biology Institute, The George Washington University, Washington, DC, United States
| | - Ignacio Ramos-Tapia
- Centro de Bioinformática y Biología Integrativa, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Zhaozhong Zhu
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Kohei Hasegawa
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Carlos A. Camargo Jr.
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Brennan Harmon
- Center for Genetic Medicine Research, Children’s National Research and Innovation Center, Washington, DC, United States
| | - Janice A. Espinola
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Laura Reck Cechinel
- Center for Genetic Medicine Research, Children’s National Research and Innovation Center, Washington, DC, United States
| | - Rachael Batabyal
- Center for Genetic Medicine Research, Children’s National Research and Innovation Center, Washington, DC, United States
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, United States
- Division of Emergency Medicine, Children’s National Hospital, Washington, DC, United States
| | - Robert J. Freishtat
- Center for Genetic Medicine Research, Children’s National Research and Innovation Center, Washington, DC, United States
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, United States
| | - Andrea Hahn
- Center for Genetic Medicine Research, Children’s National Research and Innovation Center, Washington, DC, United States
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, United States
- Division of Infectious Diseases, Children’s National Hospital, Washington, DC, United States
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4
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Sallustio F, Picerno A, Cimmarusti MT, Montenegro F, Curci C, De Palma G, Sivo C, Annese F, Fontò G, Stasi A, Pesce F, Tafuri S, Di Leo V, Gesualdo L. Elevated levels of IL-6 in IgA nephropathy patients are induced by an epigenetically driven mechanism modulated by viral and bacterial RNA. Eur J Intern Med 2023; 118:108-117. [PMID: 37550110 DOI: 10.1016/j.ejim.2023.07.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/25/2023] [Accepted: 07/31/2023] [Indexed: 08/09/2023]
Abstract
BACKGROUND Immunoglobulin A nephropathy (IgAN) is the most frequent primary glomerulonephritis and the role of IL-6 in pathogenesis is becoming increasingly important. A recent whole genome DNA methylation screening in IgAN patients identified a hypermethylated region comprising the non-coding RNA Vault RNA 2-1 (VTRNA2-1) that could explain the high IL-6 levels. METHODS The pathway leading to IL-6 secretion controlled by VTRNA2-1, PKR, and CREB was analyzed in peripheral blood mononuclear cells (PBMCs) isolated from healthy subjects (HS), IgAN patients, transplanted patients with or without IgAN. The role of double and single-strand RNA in controlling the pathway was investigated. RESULTS VTRNA2-1 was downregulated in IgAN compared to HS and in transplanted IgAN patients (TP-IgAN) compared to non-IgAN transplanted (TP). The loss of the VTRNA2-1 natural restrain in IgAN patients caused PKR hyperphosphorylation, and consequently the activation of CREB by PKR, which, in turn, led to high IL-6 production, both in IgAN and in TP-IgAN patients. IL-6 levels could be decreased by the PKR inhibitor imoxin. In addition, PKR is normally activated by bacterial and viral RNA, and we found that both the RNA poly(I:C), and the COVID-19 RNA-vaccine stimulation significantly increased the IL-6 levels in PBMCs from HS but had an opposite effect in those from IgAN patients. CONCLUSION The discovery of the upregulated VTRNA2-1/PKR/CREB/IL-6 pathway in IgAN patients may provide a novel approach to treating the disease and may be useful for the development of precision nephrology and personalized therapy by checking the VTRNA2-1 methylation level in IgAN patients.
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Affiliation(s)
- Fabio Sallustio
- Renal, Dialysis and Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari, Piazza G. Cesare, Bari 11 70124, Italy.
| | - Angela Picerno
- Department of Interdisciplinary Medicine, University of Bari "Aldo Moro", Bari, Italy
| | - Maria Teresa Cimmarusti
- Renal, Dialysis and Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari, Piazza G. Cesare, Bari 11 70124, Italy
| | - Francesca Montenegro
- Department of Interdisciplinary Medicine, University of Bari "Aldo Moro", Bari, Italy
| | - Claudia Curci
- Renal, Dialysis and Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari, Piazza G. Cesare, Bari 11 70124, Italy
| | - Giuseppe De Palma
- Institutional Biobank, Experimental Oncology and Biobank Management Unit, IRCCS Istituto Tumori Bari Giovanni Paolo II, Bari, Italy
| | - Carmen Sivo
- Renal, Dialysis and Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari, Piazza G. Cesare, Bari 11 70124, Italy
| | - Francesca Annese
- Renal, Dialysis and Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari, Piazza G. Cesare, Bari 11 70124, Italy
| | - Giulia Fontò
- Renal, Dialysis and Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari, Piazza G. Cesare, Bari 11 70124, Italy
| | - Alessandra Stasi
- Renal, Dialysis and Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari, Piazza G. Cesare, Bari 11 70124, Italy
| | - Francesco Pesce
- Renal, Dialysis and Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari, Piazza G. Cesare, Bari 11 70124, Italy
| | - Silvio Tafuri
- Department of Interdisciplinary Medicine, University of Bari "Aldo Moro", Bari, Italy
| | - Vincenzo Di Leo
- Renal, Dialysis and Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari, Piazza G. Cesare, Bari 11 70124, Italy
| | - Loreto Gesualdo
- Renal, Dialysis and Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari, Piazza G. Cesare, Bari 11 70124, Italy
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5
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Wang J, Chew BLA, Lai Y, Dong H, Xu L, Liu Y, Fu XY, Lin Z, Shi PY, Lu TK, Luo D, Jaffrey SR, Dedon PC. A systems-level mass spectrometry-based technique for accurate and sensitive quantification of the RNA cap epitranscriptome. Nat Protoc 2023; 18:2671-2698. [PMID: 37567932 DOI: 10.1038/s41596-023-00857-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 04/26/2023] [Indexed: 08/13/2023]
Abstract
Chemical modifications of transcripts with a 5' cap occur in all organisms and function in many aspects of RNA metabolism. To facilitate analysis of RNA caps, we developed a systems-level mass spectrometry-based technique, CapQuant, for accurate and sensitive quantification of the cap epitranscriptome. The protocol includes the addition of stable isotope-labeled cap nucleotides (CNs) to RNA, enzymatic hydrolysis of endogenous RNA to release CNs, and off-line enrichment of CNs by ion-pairing high-pressure liquid chromatography, followed by a 17 min chromatography-coupled tandem quadrupole mass spectrometry run for the identification and quantification of individual CNs. The total time required for the protocol can be up to 7 d. In this approach, 26 CNs can be quantified in eukaryotic poly(A)-tailed RNA, bacterial total RNA and viral RNA. This protocol can be modified to analyze other types of RNA and RNA from in vitro sources. CapQuant stands out from other methods in terms of superior specificity, sensitivity and accuracy, and it is not limited to individual caps nor does it require radiolabeling. Thanks to its unique capability of accurately and sensitively quantifying RNA caps on a systems level, CapQuant can reveal both the RNA cap landscape and the transcription start site distribution of capped RNA in a broad range of settings.
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Affiliation(s)
- Jin Wang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, People's Republic of China.
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore.
- Institute of Biomedical Sciences, Inner Mongolia University, Hohhot, China.
| | - Bing Liang Alvin Chew
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- NTU Institute of Health Technologies, Interdisciplinary Graduate Programme, Nanyang Technological University, Singapore, Singapore
| | - Yong Lai
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
- Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Hong Kong, China
| | | | - Luang Xu
- Cancer Science Institute of Singapore, Singapore, Singapore
- School of Life Science and Technology, Shanghai Institute of Biochemistry and Cell Biology, Shanghai, China
| | - Yu Liu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, People's Republic of China
| | - Xin-Yuan Fu
- Cancer Science Institute of Singapore, Singapore, Singapore
- Generos Pharmaceutical Co. Ltd, Hangzhou, China
| | - Zhenguo Lin
- Department of Biology, Saint Louis University, St. Louis, MO, USA
| | - Pei-Yong Shi
- Departments of Biochemistry & Molecular Biology and Pharmacology & Toxicology, and Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA
- GlaxoSmithKline, Rockville, MD, USA
| | - Timothy K Lu
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
- Synthetic Biology Center, Departments of Biological Engineering and Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Senti Bio, San Francisco, CA, USA
| | - Dahai Luo
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Medical College, Cornell University, New York, NY, USA
| | - Peter C Dedon
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore.
- Dept. of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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Diener C, Gibbons SM. Coarse graining the human gut microbiome. Cell Host Microbe 2023; 31:1076-1078. [PMID: 37442093 DOI: 10.1016/j.chom.2023.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 06/02/2023] [Indexed: 07/15/2023]
Abstract
The composition of the human gut microbiome is heterogeneous across people. However, if you squint, co-abundant microbial genera emerge, accounting for much of this ecological variability. In this issue of Cell Host & Microbe, Frioux et al. provide a workflow for identifying these bacterial guilds, or "enterosignatures."
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Affiliation(s)
| | - Sean M Gibbons
- Institute for Systems Biology, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; eScience Institute, University of Washington, Seattle, WA 98195, USA.
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7
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Liao X, Xia X, Yang H, Zhu Y, Deng R, Ding T. Bacterial drug-resistance and viability phenotyping upon disinfectant exposure revealed by single-nucleotide resolved-allele specific isothermal RNA amplification. J Hazard Mater 2023; 448:130800. [PMID: 36716555 PMCID: PMC9883656 DOI: 10.1016/j.jhazmat.2023.130800] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/22/2022] [Accepted: 01/14/2023] [Indexed: 06/18/2023]
Abstract
Disinfectant abuse poses a risk of bacterial evolution against stresses, especially during the coronavirus disease 2019 (COVID-19) pandemic. However, bacterial phenotypes, such as drug resistance and viability, are hard to access quickly. Here, we reported an allele specific isothermal RNA amplification (termed AlleRNA) assay, using an isothermal RNA amplification technique, i.e., nucleic acid sequence-based amplification (NASBA), integrated the amplification refractory mutation system (ARMS), involving the use of sequence-specific primers to allow the amplification of the targets with complete complementary sequences. AlleRNA assay enables rapid and simultaneous detection of the single nucleotide polymorphism (SNP) (a detection limit, a LOD of 0.5 % SNP) and the viability (a LOD of 80 CFU) of the quinolone resistant Salmonella enterica. With the use of AlleRNA assay, we found that the quinolone resistant S. enterica exhibited higher survival ability during exposure toquaternary ammonium salt, 75 % ethanol and peracetic acid, which might be attributed to the upregulation of stress response-associated genescompared with the susceptible counterparts. Additionally, the AlleRNA assay indicated the potential risk in a high-frequency occurrence of viable but nonculturable (VBNC) quinolone resistant S. enterica induced by disinfectants due to the depression of ATP biosynthesis. The excessive usage of disinfectants during the COVID-19 pandemic should be carefully evaluated due to the latent threat to ecological and human health.
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Affiliation(s)
- Xinyu Liao
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, Zhejiang 310058, China; School of Mechanical and Energy Engineering, NingboTech University, Ningbo, China; Future Food Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, 314100, Jiashan, China
| | - Xuhan Xia
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, Sichuan 610065, China
| | - Hao Yang
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, Sichuan 610065, China
| | - Yulin Zhu
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, Sichuan 610065, China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, Sichuan 610065, China.
| | - Tian Ding
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, Zhejiang 310058, China; Future Food Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, 314100, Jiashan, China.
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8
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Abstract
CRISPR-Cas systems provide resistance against foreign mobile genetic elements and have a wide range of genome editing and biotechnological applications. In this Review, we examine recent advances in understanding the molecular structures and mechanisms of enzymes comprising bacterial RNA-guided CRISPR-Cas immune systems and deployed for wide-ranging genome editing applications. We explore the adaptive and interference aspects of CRISPR-Cas function as well as open questions about the molecular mechanisms responsible for genome targeting. These structural insights reflect close evolutionary links between CRISPR-Cas systems and mobile genetic elements, including the origins and evolution of CRISPR-Cas systems from DNA transposons, retrotransposons and toxin-antitoxin modules. We discuss how the evolution and structural diversity of CRISPR-Cas systems explain their functional complexity and utility as genome editing tools.
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Affiliation(s)
- Joy Y Wang
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Patrick Pausch
- VU LSC-EMBL Partnership for Genome Editing Technologies, Life Sciences Center, Vilnius University, Vilnius, Lithuania.
| | - Jennifer A Doudna
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA.
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Gladstone Institutes, University of California, San Francisco, San Francisco, CA, USA.
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
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Hu WX, Seo EY, Cho IS, Kim JK, Song Z, Kim KH, Eom WS, Jung SH, Hammond J, Lim HS. Reassortment of Infectious Clones of Radish Mosaic Virus Shows that Systemic Necrosis in Nicotiana benthamiana Is Determined by RNA1. Phytopathology 2022; 112:1361-1372. [PMID: 35113673 DOI: 10.1094/phyto-04-21-0172-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Three infectious clones of radish mosaic virus (RaMV) were generated from isolates collected in mainland Korea (RaMV-Gg) and Jeju Island (RaMV-Aa and RaMV-Bb). These isolates differed in sequences and pathogenicity. Examination of the wild-type isolates and reassortants between the genomic RNA1 and RNA2 of these three isolates revealed that severe symptoms were associated with RNA1 of isolates Aa or Gg causing systemic necrosis in Nicotiana benthamiana, or with RNA1 of isolate Bb for induction of veinal necrosis and severe mosaic symptoms in radish. Reverse transcription, followed by quantitative real-time PCR (Q-RT-PCR), results from infected N. benthamiana confirmed that viral RNA2 accumulation level was correlated to RaMV necrosis-inducing ability, and that the RNA2 accumulation level was mostly dependent on the origin of RNA1. However, in radish, Q-RT-PCR results showed more similar viral RNA2 accumulation levels regardless of the ability of the isolate to induce necrosis. Phylogenetic analysis of genomic RNAs sequence including previously characterized isolates from North America, Europe, and Asia suggest possible recombination within RNA1, while analysis of concatenated RNA1+RNA2 sequences indicates that reassortment of RNA1 and RNA2 has been more important in the evolution of RaMV isolates than recombination. Korean isolate Aa is a potential reassortant between isolates RaMV-J and RaMV-TW, while isolate Bb might have evolved from reassortment between isolates RaMV-CA and RaMV-J. The Korean isolates were shown to also be able to infect Chinese cabbage, raising concerns that RaMV may spread from radish fields to the Chinese cabbage crop in Korea, causing further economic losses.
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Affiliation(s)
- Wen-Xing Hu
- Department of Applied Biology, Chungnam National University, Daejeon, Republic of Korea
| | - Eun-Young Seo
- Department of Applied Biology, Chungnam National University, Daejeon, Republic of Korea
| | - In-Sook Cho
- National Institute of Horticultural & Herbal Science, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Jung-Kyu Kim
- Department of Applied Biology, Chungnam National University, Daejeon, Republic of Korea
| | - Zhengxing Song
- Department of Smart Agriculture Systems, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Kang-Hee Kim
- Department of Smart Agriculture Systems, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Won-Seob Eom
- Department of Smart Agriculture Systems, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Sung-Hoon Jung
- Department of Applied Biology, Chungnam National University, Daejeon, Republic of Korea
- Department of Smart Agriculture Systems, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - John Hammond
- U.S. National Arboretum, Floral and Nursery Plants Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD 20705, U.S.A
| | - Hyoun-Sub Lim
- Department of Applied Biology, Chungnam National University, Daejeon, Republic of Korea
- Department of Smart Agriculture Systems, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
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10
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Büscher M, Horos R, Huppertz I, Haubrich K, Dobrev N, Baudin F, Hennig J, Hentze MW. Vault RNA1-1 riboregulates the autophagic function of p62 by binding to lysine 7 and arginine 21, both of which are critical for p62 oligomerization. RNA 2022; 28:742-755. [PMID: 35210358 PMCID: PMC9014876 DOI: 10.1261/rna.079129.122] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 02/09/2022] [Indexed: 05/29/2023]
Abstract
Cellular processes can be regulated at multiple levels, including transcriptional, post-transcriptional, and post-translational mechanisms. We have recently shown that the small, noncoding vault RNA1-1 negatively riboregulates p62 oligomerization in selective autophagy through direct interaction with the autophagic receptor. This function is highly specific for this Pol III transcript, but the determinants of this specificity and a mechanistic explanation of how vault RNA1-1 inhibits p62 oligomerization are lacking. Here, we combine biochemical and functional experiments to answer these questions. We show that the PB1 domain and adjacent linker region of p62 (aa 1-122) are necessary and sufficient for specific vault RNA1-1 binding, and we identify lysine 7 and arginine 21 as key hinges for p62 riboregulation. Chemical structure probing of vault RNA1-1 further reveals a central flexible loop within vault RNA1-1 that is required for the specific interaction with p62. Overall, our data provide molecular insight into how a small RNA riboregulates protein-protein interactions critical to the activation of specific autophagy.
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Affiliation(s)
- Magdalena Büscher
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Collaboration for joint Ph.D. degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Rastislav Horos
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Ina Huppertz
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Kevin Haubrich
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Nikolay Dobrev
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Florence Baudin
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Janosch Hennig
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
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11
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Janissen R, Eslami-Mossallam B, Artsimovitch I, Depken M, Dekker NH. High-throughput single-molecule experiments reveal heterogeneity, state switching, and three interconnected pause states in transcription. Cell Rep 2022; 39:110749. [PMID: 35476989 DOI: 10.1016/j.celrep.2022.110749] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 02/17/2022] [Accepted: 04/07/2022] [Indexed: 11/19/2022] Open
Abstract
Pausing by bacterial RNA polymerase (RNAp) is vital in the recruitment of regulatory factors, RNA folding, and coupled translation. While backtracking and intra-structural isomerization have been proposed to trigger pausing, our mechanistic understanding of backtrack-associated pauses and catalytic recovery remains incomplete. Using high-throughput magnetic tweezers, we examine the Escherichia coli RNAp transcription dynamics over a wide range of forces and NTP concentrations. Dwell-time analysis and stochastic modeling identify, in addition to a short-lived elemental pause, two distinct long-lived backtrack pause states differing in recovery rates. We identify two stochastic sources of transcription heterogeneity: alterations in short-pause frequency that underlies elongation-rate switching, and variations in RNA cleavage rates in long-lived backtrack states. Together with effects of force and Gre factors, we demonstrate that recovery from deep backtracks is governed by intrinsic RNA cleavage rather than diffusional Brownian dynamics. We introduce a consensus mechanistic model that unifies our findings with prior models.
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Affiliation(s)
- Richard Janissen
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Behrouz Eslami-Mossallam
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Irina Artsimovitch
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA.
| | - Martin Depken
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands.
| | - Nynke H Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands.
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12
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Abstract
Biliary atresia (BA) is a devastating liver disease in neonates. Liver fibrosis is regarded as a universal and prominent feature of BA. Studies have revealed that long non-coding RNAs (lncRNAs) regulate cellular processes during the development of liver fibrosis in BA. Long non-coding RNA-adducin 3 antisense RNA1 (lnc-ADD3-AS1) has been shown to increase susceptibility to BA. However, the role of lnc-ADD3-AS1 in liver fibrosis in BA remains unclear. Here, we investigated the role of lnc-ADD3-AS1 in the proliferation, migration, and apoptosis of the immortalized human hepatic stellate cell (HSC) line, LX-2. We successfully overexpressed and silenced lnc-ADD3-AS1 in LX-2 cells using adenovirus vectors and evaluated the proliferation of transfected cells using the Cell Counting Kit-8 (CCK8) assay. Cell apoptosis was detected using annexin V-fluorescein isothiocyanate (FITC)/propidium iodide (PI) double staining and flow cytometry. We then analyzed cell migration by performing wound-scratch and transwell migration assays. Our results show that lnc-ADD3-AS1 significantly promoted LX-2 cell proliferation and attenuated apoptosis. More importantly, lncRNA-ADD3-AS1 significantly accelerated the migration of LX-2 cells. Our data indicated that lncRNA-ADD3-AS1 plays a role in the pathogenesis of liver fibrosis in patients with BA and may serve as a potential diagnostic marker for monitoring liver fibrosis in BA or as a therapeutic target for the disease.
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Affiliation(s)
- Yongqin Ye
- Department of General Surgery, Shenzhen Children’s Hospital, Shenzhen, China
| | - Weifang Wu
- Department of Pediatric Surgery, Shantou University Medical College, Shantou, China
| | - Jiachen Zheng
- Department of Pediatric Surgery, Shantou University Medical College, Shantou, China
| | - Lihui Zhang
- Department of Traditional Chinese Medicine, Shenzhen Children’s Hospital, Shenzhen, China
- CONTACT Lihui Zhang Department of Traditional Chinese Medicine, Shenzhen Children’s Hospital, Shenzhen, China
| | - Bin Wang
- Department of General Surgery, Shenzhen Children’s Hospital, Shenzhen, China
- Bin Wang Department of General Surgery, Shenzhen Children’s Hospital, Shenzhen, China
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13
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Abstract
Small proteins encoded by open reading frames (ORFs) shorter than 50 codons (small ORFs [sORFs]) are often overlooked by annotation engines and are difficult to characterize using traditional biochemical techniques. Ribosome profiling has tremendous potential to empirically improve the annotations of prokaryotic genomes. Recent improvements in ribosome profiling methods for bacterial model organisms have revealed many new sORFs in well-characterized genomes. Antibiotics that trap ribosomes just after initiation have played a key role in these developments by allowing the unambiguous identification of the start codons (and, hence, the reading frame) for novel ORFs. Here, we describe these new methods and highlight critical controls and considerations for adapting ribosome profiling to different prokaryotic species.
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Affiliation(s)
- Nora Vazquez-Laslop
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Cynthia M. Sharma
- Molecular Infection Biology II, Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Alexander Mankin
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Allen R. Buskirk
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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14
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Duggal Y, Kurasz JE, Fontaine BM, Marotta NJ, Chauhan SS, Karls AC, Weinert EE. Cellular Effects of 2',3'-Cyclic Nucleotide Monophosphates in Gram-Negative Bacteria. J Bacteriol 2022; 204:e0020821. [PMID: 34662237 PMCID: PMC8765455 DOI: 10.1128/jb.00208-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 10/06/2021] [Indexed: 12/13/2022] Open
Abstract
Organismal adaptations to environmental stimuli are governed by intracellular signaling molecules such as nucleotide second messengers. Recent studies have identified functional roles for the noncanonical 2',3'-cyclic nucleotide monophosphates (2',3'-cNMPs) in both eukaryotes and prokaryotes. In Escherichia coli, 2',3'-cNMPs are produced by RNase I-catalyzed RNA degradation, and these cyclic nucleotides modulate biofilm formation through unknown mechanisms. The present work dissects cellular processes in E. coli and Salmonella enterica serovar Typhimurium that are modulated by 2',3'-cNMPs through the development of cell-permeable 2',3'-cNMP analogs and a 2',3'-cyclic nucleotide phosphodiesterase. Utilization of these chemical and enzymatic tools, in conjunction with phenotypic and transcriptomic investigations, identified pathways regulated by 2',3'-cNMPs, including flagellar motility and biofilm formation, and by oligoribonucleotides with 3'-terminal 2',3'-cyclic phosphates, including responses to cellular stress. Furthermore, interrogation of metabolomic and organismal databases has identified 2',3'-cNMPs in numerous organisms and homologs of the E. coli metabolic proteins that are involved in key eukaryotic pathways. Thus, the present work provides key insights into the roles of these understudied facets of nucleotide metabolism and signaling in prokaryotic physiology and suggest broad roles for 2',3'-cNMPs among bacteria and eukaryotes. IMPORTANCE Bacteria adapt to environmental challenges by producing intracellular signaling molecules that control downstream pathways and alter cellular processes for survival. Nucleotide second messengers serve to transduce extracellular signals and regulate a wide array of intracellular pathways. Recently, 2',3'-cyclic nucleotide monophosphates (2',3'-cNMPs) were identified as contributing to the regulation of cellular pathways in eukaryotes and prokaryotes. In this study, we define previously unknown cell processes that are affected by fluctuating 2',3'-cNMP levels or RNA oligomers with 2',3'-cyclic phosphate termini in E. coli and Salmonella Typhimurium, providing a framework for studying novel signaling networks in prokaryotes. Furthermore, we utilize metabolomics databases to identify additional prokaryotic and eukaryotic species that generate 2',3'-cNMPs as a resource for future studies.
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Affiliation(s)
- Yashasvika Duggal
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania, USA
| | | | | | - Nick J. Marotta
- Molecular, Cellular and Integrative Biosciences Program, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Shikha S. Chauhan
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Anna C. Karls
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Emily E. Weinert
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
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15
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Xu Z, Jin H, Duan X, Liu H, Zhao X, Fan S, Wang Y, Yao T. LncRNA PSMA3-AS1 promotes cell proliferation, migration, and invasion in ovarian cancer by activating the PI3K/Akt pathway via the miR-378a-3p/GALNT3 axis. Environ Toxicol 2021; 36:2562-2577. [PMID: 34520102 DOI: 10.1002/tox.23370] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/10/2021] [Accepted: 08/29/2021] [Indexed: 06/13/2023]
Abstract
The crucial roles of the long noncoding RNAs (lncRNAs) in the development of ovarian cancer (OC) have been extensively studied. According to the prediction result from the Kaplan-Meier Plotter database, high expression of lncRNA proteasome subunit α type-3 antisense RNA1 (PSMA3-AS1) is associated with the poor prognosis in patients with OC. Thus, the study aimed to investigate the role of lncRNA PSMA3-AS1 in OC. Reverse transcription quantitative polymerase chain reaction analysis revealed that PSMA3-AS1 expression was significantly upregulated in OC cells and tissues. PSMA3-AS1 silencing inhibited OC cell proliferation, migration, and invasion, as shown by results of cell counting kit-8, colony formation, wound healing, and Transwell assays, respectively. Additionally, PSMA3-AS1 deficiency suppressed tumor growth in vivo. Mechanistically, luciferase reporter and RNA pulldown assays implied that PSMA3-AS1 served as a competing endogenous RNA for miR-378a-3p to upregulate the expression of polypeptide N-acetylgalactosaminyltransferase 3 (GALNT3). GALNT3 was a target gene of miR-378a-3p in OC. Moreover, PSMA3-AS1 activated the PI3K/Akt pathway by upregulating GALNT3 expression. Overall, PSMA3-AS1 promotes OC cell proliferation, migration, invasion, and xenograft tumor growth by activating the PI3K/Akt pathway via the miR-378a-3p/GALNT3 axis.
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Affiliation(s)
- Zhihong Xu
- Department of Oncology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Hui Jin
- Department of Oncology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Xiaoyang Duan
- Department of Oncology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Hong Liu
- Department of Gynecology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Xiwa Zhao
- Department of Gynecology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Shaoshuang Fan
- Department of Oncology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Yan Wang
- Department of Thoracic Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Tiezhu Yao
- Department of Cardiology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
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16
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Li M, Cong Y, Qi Y, Zhang JZH. Computational Insights into the Binding Mechanism of OxyS sRNA with Chaperone Protein Hfq. Biomolecules 2021; 11:biom11111653. [PMID: 34827651 PMCID: PMC8615722 DOI: 10.3390/biom11111653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 10/16/2021] [Accepted: 10/27/2021] [Indexed: 11/16/2022] Open
Abstract
Under the oxidative stress condition, the small RNA (sRNA) OxyS that acts as essential post-transcriptional regulators of gene expression is produced and plays a regulatory function with the assistance of the RNA chaperone Hfq protein. Interestingly, experimental studies found that the N48A mutation of Hfq protein could enhance the binding affinity with OxyS while resulting in the defection of gene regulation. However, how the Hfq protein interacts with sRNA OxyS and the origin of the stronger affinity of N48A mutation are both unclear. In this paper, molecular dynamics (MD) simulations were performed on the complex structure of Hfq and OxyS to explore their binding mechanism. The molecular mechanics generalized born surface area (MM/GBSA) and interaction entropy (IE) method were combined to calculate the binding free energy between Hfq and OxyS sRNA, and the computational result was correlated with the experimental result. Per-residue decomposition of the binding free energy revealed that the enhanced binding ability of the N48A mutation mainly came from the increased van der Waals interactions (vdW). This research explored the binding mechanism between Oxys and chaperone protein Hfq and revealed the origin of the strong binding affinity of N48A mutation. The results provided important insights into the mechanism of gene expression regulation affected by protein mutations.
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Affiliation(s)
- Mengxin Li
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University at Shanghai, Shanghai 200062, China; (M.L.); (Y.C.); (Y.Q.)
| | - Yalong Cong
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University at Shanghai, Shanghai 200062, China; (M.L.); (Y.C.); (Y.Q.)
| | - Yifei Qi
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University at Shanghai, Shanghai 200062, China; (M.L.); (Y.C.); (Y.Q.)
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518000, China
| | - John Z. H. Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University at Shanghai, Shanghai 200062, China; (M.L.); (Y.C.); (Y.Q.)
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518000, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
- Department of Chemistry, New York University, New York, NY 10003, USA
- Correspondence:
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17
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Ray P, Pandey U, Das D, Aich P. Vancomycin-Induced Changes in Host Immunity and Behavior: Comparative Genomic and Metagenomic Analysis in C57BL/6 and BALB/c Mice. Dig Dis Sci 2021; 66:3776-3791. [PMID: 33386517 DOI: 10.1007/s10620-020-06729-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 11/17/2020] [Indexed: 12/21/2022]
Abstract
BACKGROUND The consequence of treatment with antibiotics on the gut microbiota can be destructive. The antibiotics, however, can be utilized to understand the role of gut microbiota on the host physiology. AIM Earlier, we reported the efficacy of vancomycin in gut microbiota perturbation. We continued to understand the effect of restoration kinetics of perturbed gut microbiota on the immunity and behavior of Th1 (C57BL/6)- and Th2 (BALB/c)-biased mice. METHODS We studied restoration kinetics of the gut microbiota for two months following the withdrawal of vancomycin treatment in both mice strains. We analyzed cecal microbiome composition, different behavioral assays, and expression of select genes associated with stress and barrier function in gut and brain. RESULTS Metagenomic analysis of gut microbiota revealed that the treatment with vancomycin caused a significant decrease in the relative abundance of Firmicutes and Bacteroidetes phyla with a time-dependent increase in Proteobacteria and Verrucomicrobia phyla. Maximum restoration (> 70%) of gut microbiota happened by the 15th day of withdrawal of vancomycin. BALB/c mice showed a more efficient restoration of gut microbiota compared to C57BL/6 mice. We established the correlation patterns of gut microbiota alteration and its effect on (a) the behavior of mice, (b) expression of key brain molecules, and (c) immunity-related genes. CONCLUSIONS The results revealed that the gut microbiome profiling, behavior, and immune responses varied significantly between Th1- and Th2-biased mice. By withdrawing the treatment with vancomycin of major gut microbes, important physiological and behavioral changes of both mice strains returned to the normal (untreated control) level.
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Affiliation(s)
- Pratikshya Ray
- School of Biological Sciences, National Institute of Science Education and Research (NISER), HBNI, P.O. - Bhimpur-Padanpur, Jatni, Khurda, Odisha, 752050, India
| | - Uday Pandey
- School of Biological Sciences, National Institute of Science Education and Research (NISER), HBNI, P.O. - Bhimpur-Padanpur, Jatni, Khurda, Odisha, 752050, India
| | - Debasmita Das
- School of Biological Sciences, National Institute of Science Education and Research (NISER), HBNI, P.O. - Bhimpur-Padanpur, Jatni, Khurda, Odisha, 752050, India
| | - Palok Aich
- School of Biological Sciences, National Institute of Science Education and Research (NISER), HBNI, P.O. - Bhimpur-Padanpur, Jatni, Khurda, Odisha, 752050, India.
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18
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Ghafoor S, Zeshan B, Khan M, Kabir S. Evaluation of 16S rRNA methyltransferase gene in aminoglycosides resistant isolates of cancer patients. Pak J Pharm Sci 2021; 34:1737-1741. [PMID: 34803010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Aminoglycosides are used in empiric treatment of critically ill patients. Efficacy of aminoglycoside has been reduced due to dissemination of resistance. The aim of this study was to evaluate aminoglycoside resistance in cancer patients with pneumoniae. A total of 150 Bronchoalveolar lavage and Bronchial washing samples were collected from cancer patients. The samples were identified with standard microbiological procedures. Phenotypic susceptibility pattern of the isolates was determined against various groups of antibiotics such as Penicillins, Cephalosporins, Carbapenems, Monobactams, Aminoglycosides, Tetracyclins, Glycopeptides and Sulphonamides. The isolates with phenotypic resistant to aminoglycosides were further evaluated for the presence of armA gene. The strains of E. coli (12.5%), S. aureus (15.6%), Streptococcus (15.6%), Pseudomonas (18.7%) and K. pneumoniae (37.5%) were isolated. The phenotypic resistance profile showed highest resistance against aminoglycosides (Tobramycin, 53.1% Gentamicin and 50% Amikacin) followed by cephalosporins and sulfonamides group. The armA gene was detected in aminoglycoside resistant isolates. The overall genotypic resistance was evaluated as 21.8%. The armA gene was found in K.pneumoniae 23.5%, Pseudomonas 11.8% (4/24) and E. coli 5.9%. High level resistance to aminoglycosides raises therapeutic concern to health care professionals. These findings highlight the importance of effective monitoring and surveillance to the use of broad-spectrum antibiotics.
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Affiliation(s)
- Saba Ghafoor
- Department of Microbiology, Faculty of Life Sciences University of the Central Punjab, Lahore, Pakistan
| | - Basit Zeshan
- Department of Microbiology, Faculty of Life Sciences University of the Central Punjab, Lahore, Pakistan
| | - Madiha Khan
- Department of Microbiology, Faculty of Life Sciences University of the Central Punjab, Lahore, Pakistan
| | - Saba Kabir
- Department of Microbiology, Faculty of Life Sciences University of the Central Punjab, Lahore, Pakistan
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19
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Ning Q, Wang D, Cheng F, Zhong Y, Ding Q, You J. Predicting rifampicin resistance mutations in bacterial RNA polymerase subunit beta based on majority consensus. BMC Bioinformatics 2021; 22:210. [PMID: 33888055 PMCID: PMC8063314 DOI: 10.1186/s12859-021-04137-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 04/16/2021] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Mutations in an enzyme target are one of the most common mechanisms whereby antibiotic resistance arises. Identification of the resistance mutations in bacteria is essential for understanding the structural basis of antibiotic resistance and design of new drugs. However, the traditionally used experimental approaches to identify resistance mutations were usually labor-intensive and costly. RESULTS We present a machine learning (ML)-based classifier for predicting rifampicin (Rif) resistance mutations in bacterial RNA Polymerase subunit β (RpoB). A total of 186 mutations were gathered from the literature for developing the classifier, using 80% of the data as the training set and the rest as the test set. The features of the mutated RpoB and their binding energies with Rif were calculated through computational methods, and used as the mutation attributes for modeling. Classifiers based on five ML algorithms, i.e. decision tree, k nearest neighbors, naïve Bayes, probabilistic neural network and support vector machine, were first built, and a majority consensus (MC) approach was then used to obtain a new classifier based on the classifications of the five individual ML algorithms. The MC classifier comprehensively improved the predictive performance, with accuracy, F-measure and AUC of 0.78, 0.83 and 0.81for training set whilst 0.84, 0.87 and 0.83 for test set, respectively. CONCLUSION The MC classifier provides an alternative methodology for rapid identification of resistance mutations in bacteria, which may help with early detection of antibiotic resistance and new drug discovery.
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Affiliation(s)
- Qing Ning
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 511443, China
| | - Dali Wang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 511443, China.
| | - Fei Cheng
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 511443, China
| | - Yuheng Zhong
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 511443, China
| | - Qi Ding
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 511443, China
| | - Jing You
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 511443, China
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Oluwagbemigun K, O'Donovan AN, Berding K, Lyons K, Alexy U, Schmid M, Clarke G, Stanton C, Cryan J, Nöthlings U. Long-term dietary intake from infancy to late adolescence is associated with gut microbiota composition in young adulthood. Am J Clin Nutr 2021; 113:647-656. [PMID: 33471048 PMCID: PMC7948843 DOI: 10.1093/ajcn/nqaa340] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 10/22/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Gut microbiota composition as influenced by long-term diet may be associated with the risk of adult chronic diseases. Thus, establishing the relation of long-term diet, particularly starting from early life, with adult microbiota composition would be an important research advance. OBJECTIVE We aimed to investigate the association of long-term intake of energy, carbohydrate, fiber, protein, and fat from infancy to late adolescence with microbiota composition in adulthood. METHODS Within the prospective DOrtmund Nutritional and Anthropometric Longitudinally Designed (DONALD) Study, we sampled stool 1 or 2 times within 1 y from 128 adults (median age: 29 y). Microbiota composition was profiled by 16S ribosomal RNA sequencing. Annual dietary records from age 1 to 18 y were retrieved. We estimated trajectories of energy, energy-adjusted carbohydrate, fiber, protein, and fat intake with multilevel models, producing predicted intake at age 1 y and rates of change in intake. A multivariate, zero-inflated, logistic-normal model was used to model the association between intake trajectories and the composition of 158 genera in single-sampled individuals. Associations found in this model were confirmed in double-sampled individuals using a zero-inflated Beta regression model. RESULTS Adjusting for covariates and temporal differences in microbiota composition, long-term carbohydrate intake was associated with 3 genera. Specifically, carbohydrate intake at age 1 y was negatively associated with Phascolarctobacterium [coefficient = -4.31; false discovery rate (FDR)-adjusted P = 0.006] and positively associated with Dialister (coefficient = 3.06; FDR-adjusted P = 0.003), and the rate of change in carbohydrate intake was positively associated with Desulfovibrio (coefficient = 13.16; FDR-adjusted P = 0.00039). Energy and other macronutrients were not associated with any genus. CONCLUSIONS This work links long-term carbohydrate intake to microbiota composition. Considering the associations of high carbohydrate intake and microbiota composition with some diseases, these findings could inform the development of gut microbiota-targeted dietary recommendations for disease prevention.
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Affiliation(s)
- Kolade Oluwagbemigun
- Unit of Nutritional Epidemiology, Department of Nutrition and Food Sciences, University of Bonn, Bonn, Germany
| | - Aoife N O'Donovan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Teagasc Moorepark Food Research Centre, Fermoy, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Kirsten Berding
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Katriona Lyons
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Teagasc Moorepark Food Research Centre, Fermoy, Ireland
| | - Ute Alexy
- Unit of Nutritional Epidemiology, Department of Nutrition and Food Sciences, University of Bonn, Bonn, Germany
| | - Matthias Schmid
- Department of Medical Biometry, Informatics, and Epidemiology, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Gerard Clarke
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- INFANT Research Centre, University College Cork, Cork, Ireland
- Department of Psychiatry and Neurobehavioral Science, University College Cork, Cork, Ireland
| | - Catherine Stanton
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Teagasc Moorepark Food Research Centre, Fermoy, Ireland
| | - John Cryan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Ute Nöthlings
- Unit of Nutritional Epidemiology, Department of Nutrition and Food Sciences, University of Bonn, Bonn, Germany
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21
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Fan H, Dong Q, Yu J, Yin L, Sun X, Yang X, Zhang W. [Knockdown of long non-coding RNA actin filament-associated protein 1 antisense RNA1 (AFAP1-AS1) inhibits epithelial-mesenchymal transition, invasion and migration of TPC-1 papillary thyroid cancer cells]. Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi 2021; 37:54-60. [PMID: 33441229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Objective To detect the expression of long non-coding RNA (lncRNA) actin filament-related protein 1 antisense RNA1 (AFAP1-AS1) in papillary thyroid carcinoma tissue, and to investigate the effects of the knockdown of AFAP1-AS1 in TPC-1 papillary thyroid carcinoma cells on cell epithelial-mesenchymal transition (EMT) and related molecular mechanism in TPC-1 cells. Methods Real-time quantitative PCR was used to detect the expression of lncRNA AFAP1-AS1 in 60 cases of papillary thyroid carcinoma tissues. RNA interfering (RNAi) was used to knockdown AFAP1-AS1 in TPC-1 cells. TPC-1 cells were divided into AFAP1-AS1 knockdown (shAFAP1-AS1) group, negative control RNA (shNC) group and untransfected control group. The colony-formation assay, TranswellTM invasion and scratch healing assays were employed to detect the colony-forming ability, cell invasion ability and cell migration ability of TPC-1 cells, respectively. After knockdown of AFAP1-AS1, real-time quantitative PCR and Western blot analysis were used to detect the mRNA and protein levels of E-cadherin, vimentin, β-catenin and snail2, respectively. Results Compared with the paracancerous tissue, the expression level of AFAP1-AS1 mRNA in the papillary thyroid carcinoma tissue significantly increased. Knockdown of AFAP1-AS1 significantly reduced the colony-forming ability, invasion and migration ability of TPC-1 cells. Compared with shNC group and control group, knockdown of AFAP1-AS1 significantly reduced the mRNA and protein expression of snail2, vimentin and β-catenin. In contrast, the mRNA and protein expression of E-cadherin increased considerably. Conclusion The lncRNA AFAP1-AS1 is highly expressed in papillary thyroid carcinoma tissue. After knockdown of AFAP1-AS1 in TPC-1 cells, the colony-forming ability, invasion and migration ability of cancer cells are significantly down-regulated, which may be related to the inhibition of EMT.
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Affiliation(s)
- Huijie Fan
- Department of Endocrinology and Metabolism, Zhengzhou People's Hospital, Zhengzhou 450000, China
| | - Qijuan Dong
- Department of Endocrinology and Metabolism, Zhengzhou People's Hospital, Zhengzhou 450000, China. *Corresponding author, E-mail:
| | - Jianghong Yu
- Department of Endocrinology and Metabolism, Zhengzhou People's Hospital, Zhengzhou 450000, China
| | - Lu Yin
- Department of Endocrinology and Metabolism, Zhengzhou People's Hospital, Zhengzhou 450000, China
| | - Xiaofei Sun
- Department of Endocrinology and Metabolism, Zhengzhou People's Hospital, Zhengzhou 450000, China
| | - Xue Yang
- Department of Endocrinology and Metabolism, Zhengzhou People's Hospital, Zhengzhou 450000, China
| | - Wenyu Zhang
- Department of Endocrinology and Metabolism, Zhengzhou People's Hospital, Zhengzhou 450000, China
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22
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Banta AB, Enright AL, Siletti C, Peters JM. A High-Efficacy CRISPR Interference System for Gene Function Discovery in Zymomonas mobilis. Appl Environ Microbiol 2020; 86:e01621-20. [PMID: 32978126 PMCID: PMC7657623 DOI: 10.1128/aem.01621-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 09/20/2020] [Indexed: 01/23/2023] Open
Abstract
Zymomonas mobilis is a promising biofuel producer due to its high alcohol tolerance and streamlined metabolism that efficiently converts sugar to ethanol. Z. mobilis genes are poorly characterized relative to those of model bacteria, hampering our ability to rationally engineer the genome with pathways capable of converting sugars from plant hydrolysates into valuable biofuels and bioproducts. Many of the unique properties that make Z. mobilis an attractive biofuel producer are controlled by essential genes; however, these genes cannot be manipulated using traditional genetic approaches (e.g., deletion or transposon insertion) because they are required for viability. CRISPR interference (CRISPRi) is a programmable gene knockdown system that can precisely control the timing and extent of gene repression, thus enabling targeting of essential genes. Here, we establish a stable, high-efficacy CRISPRi system in Z. mobilis that is capable of perturbing all genes-including essential genes. We show that Z. mobilis CRISPRi causes either strong knockdowns (>100-fold) using single guide RNA (sgRNA) spacers that perfectly match target genes or partial knockdowns using spacers with mismatches. We demonstrate the efficacy of Z. mobilis CRISPRi by targeting essential genes that are universally conserved in bacteria, are key to the efficient metabolism of Z. mobilis, or underlie alcohol tolerance. Our Z. mobilis CRISPRi system will enable comprehensive gene function discovery, opening a path to rational design of biofuel production strains with improved yields.IMPORTANCE Biofuels produced by microbial fermentation of plant feedstocks provide renewable and sustainable energy sources that have the potential to mitigate climate change and improve energy security. Engineered strains of the bacterium Z. mobilis can convert sugars extracted from plant feedstocks into next-generation biofuels like isobutanol; however, conversion by these strains remains inefficient due to key gaps in our knowledge about genes involved in metabolism and stress responses such as alcohol tolerance. Here, we develop CRISPRi as a tool to explore gene function in Z. mobilis We characterize genes that are essential for growth, required to ferment sugar to ethanol, and involved in resistance to isobutanol. Our Z. mobilis CRISPRi system makes it straightforward to define gene function and can be applied to improve strain engineering and increase biofuel yields.
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Affiliation(s)
- Amy B Banta
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Amy L Enright
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Cheta Siletti
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jason M Peters
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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Lott SC, Voigt K, Lambrecht SJ, Hess WR, Steglich C. A framework for the computational prediction and analysis of non-coding RNAs in microbial environmental populations and their experimental validation. ISME J 2020; 14:1955-1965. [PMID: 32346084 PMCID: PMC7368042 DOI: 10.1038/s41396-020-0658-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 03/22/2020] [Accepted: 04/07/2020] [Indexed: 11/09/2022]
Abstract
Small regulatory RNAs and antisense RNAs play important roles in the regulation of gene expression in bacteria but are underexplored, especially in natural populations. While environmentally relevant microbes often are not amenable to genetic manipulation or cannot be cultivated in the laboratory, extensive metagenomic and metatranscriptomic datasets for these organisms might be available. Hence, dedicated workflows for specific analyses are needed to fully benefit from this information. Here, we identified abundant sRNAs from oceanic environmental populations of the ecologically important primary producer Prochlorococcus starting from a metatranscriptomic differential RNA-Seq (mdRNA-Seq) dataset. We tracked their homologs in laboratory isolates, and we provide a framework for their further detailed characterization. Several of the experimentally validated sRNAs responded to ecologically relevant changes in cultivation conditions. The expression of the here newly discovered sRNA Yfr28 was highly stimulated in low-nitrogen conditions. Its predicted top targets include mRNAs encoding cell division proteins, a sigma factor, and several enzymes and transporters, suggesting a pivotal role of Yfr28 in the coordination of primary metabolism and cell division. A cis-encoded antisense RNA was identified as a possible positive regulator of atpF encoding subunit b' of the ATP synthase complex. The presented workflow will also be useful for other environmentally relevant microorganisms for which experimental validation abilities are frequently limiting although there is wealth of sequence information available.
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Affiliation(s)
- Steffen C Lott
- University of Freiburg, Faculty of Biology, D-79104, Freiburg, Germany
| | - Karsten Voigt
- University of Freiburg, Faculty of Biology, D-79104, Freiburg, Germany
| | - S Joke Lambrecht
- University of Freiburg, Faculty of Biology, D-79104, Freiburg, Germany
| | - Wolfgang R Hess
- University of Freiburg, Faculty of Biology, D-79104, Freiburg, Germany
| | - Claudia Steglich
- University of Freiburg, Faculty of Biology, D-79104, Freiburg, Germany.
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24
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Kang W, Jiang Z, Chen Y, Wu F, Liu C, Wang H, Shi S, Zhang XX. Plant transcriptome analysis reveals specific molecular interactions between alfalfa and its rhizobial symbionts below the species level. BMC Plant Biol 2020; 20:293. [PMID: 32590947 PMCID: PMC7318466 DOI: 10.1186/s12870-020-02503-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 06/18/2020] [Indexed: 05/22/2023]
Abstract
BACKGROUND Leguminous plants alter patterns of gene expression in response to symbiotic colonization and infection by their cognate rhizobial bacteria, but the extent of the transcriptomic response has rarely been examined below the species level. Here we describe the identification of 12 rhizobial biotypes of Ensifer meliloti, which form nitrogen-fixing nodules in the roots of alfalfa (Medicago sativa L.), followed by a comparative RNA-seq analysis of four alfalfa cultivars each inoculated with two E. meliloti strains varying in symbiotic performance and phylogenetic relatedness. RESULTS Rhizobial biotypes were identified on the basis of their symbiotic performance, particularly shoot dry weight. Differentially expressed genes (DEGs) and metabolic pathways were determined by comparing the RNA-seq data with that of the uninoculated control plant. Significant differences were found between DEGs generated in each cultivar with the inoculation of two rhizobial strains in comparison (P < 0.01). A total of 8111 genes was differentially expressed, representing ~ 17.1% of the M. sativa genome. The proportion of DEGs ranges from 0.5 to 12.2% for each alfalfa cultivar. Interestingly, genes with predicted roles in flavonoid biosynthesis and plant-pathogen interaction (NBS-LRR) were identified as the most significant DEGs. Other DEGs include Medsa002106 and genes encoding nodulins and NCR peptides whose expression is specifically induced during the development of nitrogen-fixing nodules. More importantly, strong significant positive correlations were observed between plant transcriptomes (DEGs and KEGG pathways) and phylogenetic distances between the two rhizobial inoculants. CONCLUSIONS Alfalfa expresses significantly distinct sets of genes in response to infection by different rhizobial strains at the below-species levels (i.e. biotype or strain). Candidate genes underlying the specific interactions include Medsa002106 and those encoding nodulins and NCR peptides and proteins in the NBS-LRR family.
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Affiliation(s)
- Wenjuan Kang
- College of Grassland Science, Gansu Agricultural University, Lanzhou, 730070, China
- School of Natural and Computational Sciences, Massey University at Albany, Auckland, 0745, New Zealand
| | - Zhehao Jiang
- College of Grassland Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yonggang Chen
- College of Grassland Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Fang Wu
- College of Grassland Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Chang Liu
- College of Grassland Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Haifang Wang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Shangli Shi
- College of Grassland Science, Gansu Agricultural University, Lanzhou, 730070, China.
- Key Laboratory of Grassland Ecosystem of the Chinese Ministry of Education, Lanzhou, 730070, China.
| | - Xue-Xian Zhang
- School of Natural and Computational Sciences, Massey University at Albany, Auckland, 0745, New Zealand
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Wang X, Li W, Zhou Q, Li J, Wang X, Zhang J, Li D, Qi X, Liu T, Zhao X, Li S, Yang L, Xie L. MANF Promotes Diabetic Corneal Epithelial Wound Healing and Nerve Regeneration by Attenuating Hyperglycemia-Induced Endoplasmic Reticulum Stress. Diabetes 2020; 69:1264-1278. [PMID: 32312869 DOI: 10.2337/db19-0835] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 03/15/2020] [Indexed: 11/13/2022]
Abstract
Mesencephalic astrocyte-derived neurotrophic factor (MANF) is a neurotrophic factor widely expressed in mammalian tissues, and it exerts critical protective effects on neurons and other cell types in various disease models, such as those for diabetes. However, to date, the expression and roles of MANF in the cornea, with or without diabetic keratopathy (DK), remain unclear. Here, we demonstrate that MANF is abundantly expressed in normal corneal epithelial cells; however, MANF expression was significantly reduced in both unwounded and wounded corneal epithelium in streptozotocin-induced type 1 diabetic C57BL/6 mice. Recombinant human MANF significantly promoted normal and diabetic corneal epithelial wound healing and nerve regeneration. Furthermore, MANF inhibited hyperglycemia-induced endoplasmic reticulum (ER) stress and ER stress-mediated apoptosis. Attenuation of ER stress with 4-phenylbutyric acid (4-PBA) also ameliorated corneal epithelial closure and nerve regeneration. However, the beneficial effects of MANF and 4-PBA were abolished by an Akt inhibitor and Akt-specific small interfering RNA (siRNA). Finally, we reveal that the subconjunctival injection of MANF-specific siRNA prevents corneal epithelial wound healing and nerve regeneration. Our results provide important evidence that hyperglycemia-suppressed MANF expression may contribute to delayed corneal epithelial wound healing and impaired nerve regeneration by increasing ER stress, and MANF may be a useful therapeutic modality for treating DK.
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Affiliation(s)
- Xiaochuan Wang
- School of Medicine and Life Sciences, University of Jinan-Shandong Academy of Medical Sciences, Jinan, Shandong, China
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Qingdao, Shandong, China
| | - Weina Li
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Qingdao, Shandong, China
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Qingjun Zhou
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Qingdao, Shandong, China
| | - Jing Li
- School of Medicine and Life Sciences, University of Jinan-Shandong Academy of Medical Sciences, Jinan, Shandong, China
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Qingdao, Shandong, China
| | - Xiaolei Wang
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Qingdao, Shandong, China
| | - Jing Zhang
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Qingdao, Shandong, China
| | - Dewei Li
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Qingdao, Shandong, China
| | - Xia Qi
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Qingdao, Shandong, China
| | - Ting Liu
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Qingdao, Shandong, China
| | - Xiaowen Zhao
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Qingdao, Shandong, China
| | - Suxia Li
- Shandong Eye Hospital, Shandong Eye Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Lingling Yang
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Qingdao, Shandong, China
| | - Lixin Xie
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Qingdao, Shandong, China
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Shobo CO, Alisoltani A, Abia ALK, Mtshali PS, Ismail A, Zishiri O, Horn JD, Brysiewicz P, Essack SY, Bester LA. Bacterial diversity and functional profile of microbial populations on surfaces in public hospital environments in South Africa: A high throughput metagenomic analysis. Sci Total Environ 2020; 719:137360. [PMID: 32114226 DOI: 10.1016/j.scitotenv.2020.137360] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/14/2020] [Accepted: 02/14/2020] [Indexed: 06/10/2023]
Abstract
With the introduction of the One Health approach to global health advocated by the World Health Organization, the role of the environment as a reservoir and transmission route for diverse microorganisms is increasingly being recognised globally. This study investigated the diversity and functional profiles of bacterial communities using high-throughput metagenomics of the 16S rRNA gene in samples collected from environmental surfaces in different levels of healthcare in South Africa. A total of 150 samples were collected in three public hospitals [District (A), Regional (C) and Central (B)] from intensive care and paediatric wards. Military hospitals were excluded. Swabs were taken from mattresses, drip stands, ward telephones, patient files and sinks. A total of 7,996,346 reads were found, of which 7,319,569 were quality-filtered reads. Unique (and shared) microbial community structures were identified within the different hospital levels, locations and sample source. A total of 11 phyla, 29 classes, 50 orders, 105 families, 190 genera and 288 known species were identified. The primary phyla identified were Proteobacteria, Firmicutes and Actinobacteria. The dominant class identified was Gamma-proteobacteria, followed by Bacilli and Actinobacteria. Acinetobacter (16.08%), Citrobacter (13.64%), Staphylococcus (9.65%) and Corynebacterium (6.15%) were predominant genera. Although the functional profile analysis identified citrate cycle (TCA), signal transduction mechanisms, bisphenol degradation, tyrosine metabolism and transcription-factors as the dominant pathways, human disease functional classes, including involvement in antibiotic resistance, were significantly identified. The drip stands, patient files and ward telephones in all the wards of Hospitals A and C contained a higher number of human diseases functional classes. These findings highlight the potential of different hospital environments to serve as reservoirs and possible sources of bacterial pathogens; thus, the need for better monitoring and hygienic practices within the hospital environment.
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Affiliation(s)
- Christiana Omowunmi Shobo
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Department of Medical Microbiology, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa
| | - Arghavan Alisoltani
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA, USA
| | - Akebe Luther King Abia
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Philip Senzo Mtshali
- Sequencing Core Facility, National Institute for Communicable Diseases, Division of National Health Laboratory Service, Sandringham, Johannesburg, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, Division of National Health Laboratory Service, Sandringham, Johannesburg, South Africa
| | - Oliver Zishiri
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban 4000, South Africa
| | - Juliana Deidre Horn
- South Africa Military Health Service, Area Military Health Care, KwaZulu-Natal, Durban, South Africa
| | - Petra Brysiewicz
- Discipline of Nursing, School of Nursing & Public Health, University of KwaZulu-Natal, Durban, South Africa
| | - Sabiha Yusuf Essack
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Linda Antoinette Bester
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
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Bao C, Loerch S, Ling C, Korostelev AA, Grigorieff N, Ermolenko DN. mRNA stem-loops can pause the ribosome by hindering A-site tRNA binding. eLife 2020; 9:e55799. [PMID: 32427100 PMCID: PMC7282821 DOI: 10.7554/elife.55799] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 05/18/2020] [Indexed: 12/27/2022] Open
Abstract
Although the elongating ribosome is an efficient helicase, certain mRNA stem-loop structures are known to impede ribosome movement along mRNA and stimulate programmed ribosome frameshifting via mechanisms that are not well understood. Using biochemical and single-molecule Förster resonance energy transfer (smFRET) experiments, we studied how frameshift-inducing stem-loops from E. coli dnaX mRNA and the gag-pol transcript of Human Immunodeficiency Virus (HIV) perturb translation elongation. We find that upon encountering the ribosome, the stem-loops strongly inhibit A-site tRNA binding and ribosome intersubunit rotation that accompanies translation elongation. Electron cryo-microscopy (cryo-EM) reveals that the HIV stem-loop docks into the A site of the ribosome. Our results suggest that mRNA stem-loops can transiently escape the ribosome helicase by binding to the A site. Thus, the stem-loops can modulate gene expression by sterically hindering tRNA binding and inhibiting translation elongation.
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Affiliation(s)
- Chen Bao
- Department of Biochemistry and Biophysics at School of Medicine and Dentistry and Center for RNA Biology, University of RochesterRochesterUnited States
| | - Sarah Loerch
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Clarence Ling
- Department of Biochemistry and Biophysics at School of Medicine and Dentistry and Center for RNA Biology, University of RochesterRochesterUnited States
| | - Andrei A Korostelev
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical SchoolWorcesterUnited States
- RNA Therapeutics Institute, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Nikolaus Grigorieff
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
- RNA Therapeutics Institute, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Dmitri N Ermolenko
- Department of Biochemistry and Biophysics at School of Medicine and Dentistry and Center for RNA Biology, University of RochesterRochesterUnited States
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Joglekar P, Mesa CP, Richards VA, Polson SW, Wommack KE, Fuhrmann JJ. Polyphasic analysis reveals correlation between phenotypic and genotypic analysis in soybean bradyrhizobia (Bradyrhizobium spp.). Syst Appl Microbiol 2020; 43:126073. [PMID: 32139173 PMCID: PMC7894101 DOI: 10.1016/j.syapm.2020.126073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 02/07/2020] [Accepted: 02/09/2020] [Indexed: 10/25/2022]
Abstract
Soybean bradyrhizobia (Bradyrhizobium spp.) are bacteria that fix atmospheric nitrogen within the root nodules of soybean, a crop critical for meeting global nutritional protein demand. Members of this group differ in symbiotic effectiveness, and historically both phenotypic and genotypic approaches have been used to assess bradyrhizobial diversity. However, agreement between various approaches of assessment is poorly known. A collection (n=382) of soybean bradyrhizobia (Bradyrhizobium japonicum, B. diazoefficiens, and B. elkanii) were characterized by Internal Transcribed Spacer - Restriction Fragment Length Polymorphism (ITS-RFLP), cellular fatty acid composition (fatty acid methyl esters, FAME), and serological reactions to assess agreement between phenotypic and genotypic methods. Overall, 76% of the accessions demonstrated identical clustering with each of these techniques. FAME was able to identify all 382 accessions, whereas 14% were non-reactive serologically. One ITS-RFLP group, containing 36 Delaware isolates, produced multiple ITS amplicons indicating they possess multiple ribosomal RNA (rrn) operons. Cloning and sequencing revealed that these strains contained as many as three heterogenous rrn operons, a trait previously unknown in bradyrhizobia. A representative subset of 96 isolates was further characterized using 16S rRNA and Internal Transcribed Spacer (ITS) amplicon sequencing. ITS sequences showed better inter- and intra-species discrimination (65-99% identity) than 16S sequences (96-99% identity). This study shows that phenotypic and genotypic approaches are strongly correlated at the species level but should be approached with caution. We also suggest using combined 16S and ITS genotyping data to obtain better inter- and intra-species resolution in bradyrhizobia classification.
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Affiliation(s)
- P Joglekar
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
| | - C P Mesa
- Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware, USA
| | - V A Richards
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
| | - S W Polson
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware, USA; Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, USA
| | - K E Wommack
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA; Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware, USA; Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, USA
| | - J J Fuhrmann
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA; Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware, USA.
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Yang Y, Xing S, Li S, Niu Y, Li C, Huang T, Liao X. Potential regulation of small RNAs on bacterial function activities in pig farm wastewater treatment plants. J Environ Sci (China) 2020; 91:292-300. [PMID: 32172978 DOI: 10.1016/j.jes.2020.02.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 02/01/2020] [Accepted: 02/11/2020] [Indexed: 06/10/2023]
Abstract
Small RNAs (sRNAs) are key players in the regulation of bacterial gene expression. However, the distribution and regulatory functions of sRNA in pig farm wastewater treatment plants (WWTPs) remains unknown. In this study, the wastewaters in anoxic and oxic tanks of the WWTPs were collected. The profiles of the community structure, mRNA expression, and sRNA expression of bacteria in pig farm wastewater were investigated using transcriptome sequencing and qPCR. This study demonstrated that there was a higher abundance of sRNA in the pig farm WWTPs and 52 sRNAs were detected. The sRNAs were mainly present in Proteobacteria and Firmicutes, including the potential human pathogenic bacteria (HPB) (Escherichia, Shigella, Bordetella and Morganella), crop pathogen (Pectobacterium) and denitrifying bacteria (Zobellella). And the sRNAs were involved in the bacterial functional activities such as translation, transcription, drug resistance, membrane transport and amino acid metabolism. In addition, most sRNAs had a higher abundance in anoxic tanks which contained a higher abundance of the genes associated with infectious diseases and drug resistance than that in oxic tanks. The results presented here show that in pig farm WWTPs, sRNA played an important role in bacterial function activities, especially the infectious diseases, drug resistance and denitrification, which can provide a new point of penetration for improving the pig farm WWTPs.
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Affiliation(s)
- Yiwen Yang
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Sicheng Xing
- Key Laboratory of Tropical Agricultural Environment, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Sumin Li
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Yajing Niu
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Cheng Li
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Tuoxin Huang
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Xindi Liao
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Tropical Agricultural Environment, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agriculture University, Guangzhou 510642, China.
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Naha A, Mandal RS, Samanta P, Saha RN, Shaw S, Ghosh A, Chatterjee NS, Dutta P, Okamoto K, Dutta S, Mukhopadhyay AK. Deciphering the possible role of ctxB7 allele on higher production of cholera toxin by Haitian variant Vibrio cholerae O1. PLoS Negl Trop Dis 2020; 14:e0008128. [PMID: 32236098 PMCID: PMC7112172 DOI: 10.1371/journal.pntd.0008128] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 02/10/2020] [Indexed: 12/16/2022] Open
Abstract
Cholera continues to be an important public health concern in developing countries where proper hygiene and sanitation are compromised. This severe diarrheal disease is caused by the Gram-negative pathogen Vibrio cholerae belonging to serogroups O1 and O139. Cholera toxin (CT) is the prime virulence factor and is directly responsible for the disease manifestation. The ctxB gene encodes cholera toxin B subunit (CTB) whereas the A subunit (CTA) is the product of ctxA gene. Enzymatic action of CT depends on binding of B pentamers to the lipid-based receptor ganglioside GM1. In recent years, emergence of V. cholerae Haitian variant strains with ctxB7 allele and their rapid spread throughout the globe has been linked to various cholera outbreaks in Africa and Asia. These strains produce classical type (WT) CTB except for an additional mutation in the signal sequence region where an asparagine (N) residue replaces a histidine (H) at the 20th amino acid position (H20N) of CTB precursor (pre-CTB). Here we report that Haitian variant V. cholerae O1 strains isolated in Kolkata produced higher amount of CT compared to contemporary O1 El Tor variant strains under in vitro virulence inducing conditions. We observed that the ctxB7 allele, itself plays a pivotal role in higher CT production. Based on our in silico analysis, we hypothesized that higher accumulation of toxin subunits from ctxB7 allele might be attributed to the structural alteration at the CTB signal peptide region of pre-H20N CTB. Overall, this study provides plausible explanation regarding the hypertoxigenic phenotype of the Haitian variant strains which have spread globally, possibly through positive selection for increased pathogenic traits.
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Affiliation(s)
- Arindam Naha
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Rahul Shubhra Mandal
- Biomedical Informatics Center, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Prosenjit Samanta
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Rudra Narayan Saha
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Sreeja Shaw
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Amit Ghosh
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | | | - Pujarini Dutta
- Division of Clinical Medicine, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Keinosuke Okamoto
- Collaborative Research Center of Okayama University for Infectious Diseases at NICED, Kolkata, India
| | - Shanta Dutta
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Asish Kumar Mukhopadhyay
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
- * E-mail:
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Ami VKG, Balasubramanian R, Hegde SR. Genome-wide identification of the context-dependent sRNA expression in Mycobacterium tuberculosis. BMC Genomics 2020; 21:167. [PMID: 32070281 PMCID: PMC7029489 DOI: 10.1186/s12864-020-6573-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 02/10/2020] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Tuberculosis remains one of the leading causes of morbidity and mortality worldwide. Therefore, understanding the pathophysiology of Mycobacterium tuberculosis is imperative for developing new drugs. Post-transcriptional regulation plays a significant role in microbial adaptation to different growth conditions. While the proteins associated with gene expression regulation have been extensively studied in the pathogenic strain M. tuberculosis H37Rv, post-transcriptional regulation involving small RNAs (sRNAs) remains poorly understood. RESULTS We developed a novel moving-window based approach to detect sRNA expression using RNA-Seq data. Overlaying ChIP-seq data of RNAP (RNA Polymerase) and NusA suggest that these putative sRNA coding regions are significantly bound by the transcription machinery. Besides capturing many experimentally validated sRNAs, we observe the context-dependent expression of novel sRNAs in the intergenic regions of M. tuberculosis genome. For example, ncRv11806 shows expression only in the stationary phase, suggesting its role in mycobacterial latency which is a key attribute to long term pathogenicity. Also, ncRv11875C showed expression in the iron-limited condition, which is prevalent inside the macrophages of the host cells. CONCLUSION The systems level analysis of sRNA highlights the condition-specific expression of sRNAs which might enable the pathogen survival by rewiring regulatory circuits.
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Affiliation(s)
- Vimla Kany G Ami
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, 560 100, India
| | - Rami Balasubramanian
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, 560 100, India
| | - Shubhada R Hegde
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, 560 100, India.
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Abstract
Chimeric RNAs are the transcripts composed of exons from two separate genes or transcripts. Although the presence of these joined RNA molecules have mainly been documented in a variety of eukaryotes, we recently demonstrated that the Ll.LtrB group II intron, from the gram-positive bacterium Lactococcus lactis, can generate chimeric mRNAs through a novel intergenic trans-splicing pathway. Here we describe the detailed experimental procedures to detect group II intron-generated mRNA-mRNA chimeras from total RNA extracts using stringent reverse transcription conditions along with a reverse splicing-deficient group II intron as a negative control.
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Affiliation(s)
| | - Caroline Monat
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada
| | - Benoit Cousineau
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada.
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Lasa A, di Cesare A, Tassistro G, Borello A, Gualdi S, Furones D, Carrasco N, Cheslett D, Brechon A, Paillard C, Bidault A, Pernet F, Canesi L, Edomi P, Pallavicini A, Pruzzo C, Vezzulli L. Dynamics of the Pacific oyster pathobiota during mortality episodes in Europe assessed by 16S rRNA gene profiling and a new target enrichment next-generation sequencing strategy. Environ Microbiol 2019; 21:4548-4562. [PMID: 31325353 PMCID: PMC7379488 DOI: 10.1111/1462-2920.14750] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/12/2019] [Accepted: 07/14/2019] [Indexed: 02/05/2023]
Abstract
Infectious agents such as the bacteria Vibrio aestuarianus or Ostreid herpesvirus 1 have been repeatedly associated with dramatic disease outbreaks of Crassostrea gigas beds in Europe. Beside roles played by these pathogens, microbial infections in C. gigas may derive from the contribution of a larger number of microorganisms than previously thought, according to an emerging view supporting the polymicrobial nature of bivalve diseases. In this study, the microbial communities associated with a large number of C. gigas samples collected during recurrent mortality episodes at different European sites were investigated by real-time PCR and 16SrRNA gene-based microbial profiling. A new target enrichment next-generation sequencing protocol for selective capturing of 884 phylogenetic and virulence markers of the potential microbial pathogenic community in oyster tissue was developed allowing high taxonomic resolution analysis of the bivalve pathobiota. Comparative analysis of contrasting C. gigas samples conducted using these methods revealed that oyster experiencing mortality outbreaks displayed signs of microbiota disruption associated with the presence of previously undetected potential pathogenic microbial species mostly belonging to genus Vibrio and Arcobacter. The role of these species and their consortia should be targeted by future studies aiming to shed light on mechanisms underlying polymicrobial infections in C. gigas.
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Affiliation(s)
- Aide Lasa
- Department of Earth, Environmental and Life Sciences (DISTAV)University of GenoaGenoaItaly
- Department of Microbiology and ParasitologyUniversidade de Santiago de CompostelaSantiago de CompostelaSpain
| | - Andrea di Cesare
- National Research Council‐Water Research Institute (CNR‐IRSA), Largo Tonolli 50, 28822VerbaniaItaly
| | - Giovanni Tassistro
- Department of Earth, Environmental and Life Sciences (DISTAV)University of GenoaGenoaItaly
| | - Alessio Borello
- Department of Earth, Environmental and Life Sciences (DISTAV)University of GenoaGenoaItaly
| | - Stefano Gualdi
- Department of Plant and Microbial BiologyUniversity of ZürichZürichSwitzerland
| | | | | | - Deborah Cheslett
- Fish Health UnitThe Marine Institute, Rinville OranmoreGalwayIreland
| | - Amanda Brechon
- Fish Health UnitThe Marine Institute, Rinville OranmoreGalwayIreland
| | - Christine Paillard
- Laboratoire des sciences de l'Environnement Marin, Institut Universitaire Européen de la MUniversité de Bretagne Occidentale – UMR6539 CNRS/UBO/IRD/IfremerPlouzanéFrance
| | - Adeline Bidault
- Laboratoire des sciences de l'Environnement Marin, Institut Universitaire Européen de la MUniversité de Bretagne Occidentale – UMR6539 CNRS/UBO/IRD/IfremerPlouzanéFrance
| | - Fabrice Pernet
- Ifremer, Physiologie Fonctionnelle des Organismes MarinsUMR 6539 LEMAR (CNRS/Ifremer/IRD/UBO) Technopole Iroise, CS 1007029280PlouzaneFrance
| | - Laura Canesi
- Department of Earth, Environmental and Life Sciences (DISTAV)University of GenoaGenoaItaly
| | - Paolo Edomi
- Department of Life SciencesUniversity of TriesteTriesteItaly
| | | | - Carla Pruzzo
- Department of Earth, Environmental and Life Sciences (DISTAV)University of GenoaGenoaItaly
| | - Luigi Vezzulli
- Department of Earth, Environmental and Life Sciences (DISTAV)University of GenoaGenoaItaly
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Eggers S, Safdar N, Sethi AK, Suen G, Peppard PE, Kates AE, Skarlupka JH, Kanarek M, Malecki KMC. Urinary lead concentration and composition of the adult gut microbiota in a cross-sectional population-based sample. Environ Int 2019; 133:105122. [PMID: 31518933 PMCID: PMC7230144 DOI: 10.1016/j.envint.2019.105122] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 08/22/2019] [Accepted: 08/22/2019] [Indexed: 05/09/2023]
Abstract
BACKGROUND Lead (Pb) is a ubiquitous environmental contaminant with an array of detrimental health effects in children and adults, including neurological and immune dysfunction. Emerging evidence suggests that Pb exposure may alter the composition of the gut microbiota, however few studies have examined this association in human populations. The purpose of this study was to examine the association between urinary Pb concentration and the composition of the adult gut microbiota in a population-based sample of adults. METHODS Data used in this study were collected as part of the Survey of the Health of Wisconsin (SHOW) and its ancillary microbiome study. The SHOW is a household-based health examination survey of Wisconsin residents, collecting a variety of survey data on health determinants and outcomes, as well as objective measurements of body habitus, and biological specimens including urine. The ancillary microbiome study added additional questions and biological specimen collection, including stool, from participants age 18+. Pb concentration was analyzed in urine samples, and gut microbiota composition was assessed using DNA sequencing of the 16S rRNA V4 region, extracted from stool samples. Data processing and statistical analyses were performed in mothur, Python, R, and SAS. RESULTS Of 696 participants, urinary Pb concentration was highest in those age 70+, females, those with a high school diploma or lower, current and former smokers, and those without indoor pets. In adjusted models, increasing urinary Pb levels were associated with increases in microbial α-diversity (p = 0.071) and richness (p = 0.005). Differences in microbial β-diversity were significantly associated (p = 0.003) with differences in urinary Pb level. Presence of Proteobacteria, including members of the Burkholderiales, was significantly associated with increased urinary Pb. CONCLUSION These results suggest that Pb exposure is associated with differences in the composition of the adult gut microbiota in a population-based human sample. Further investigation of this association is warranted.
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Affiliation(s)
- Shoshannah Eggers
- Department of Population Health Sciences, School of Medicine and Public Health, University of Wisconsin - Madison, 610 Walnut St, WARF 707, Madison, WI 53726, USA; Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1057, New York, NY 10029, USA.
| | - Nasia Safdar
- Division of Infectious Disease, Department of Medicine, School of Medicine and Public Health, University of Wisconsin - Madison, UW Med Fndtn Centennial Bldg, 1685 Highland Ave, Madison, WI 53705, USA; William S. Middleton Veterans Affairs Medical Center, 2500 Overlook Terrace, Madison, WI 53705, USA.
| | - Ajay K Sethi
- Department of Population Health Sciences, School of Medicine and Public Health, University of Wisconsin - Madison, 610 Walnut St, WARF 707, Madison, WI 53726, USA.
| | - Garret Suen
- Department of Bacteriology, University of Wisconsin - Madison, 1550 Linden Dr, Madison, WI 53706, USA.
| | - Paul E Peppard
- Department of Population Health Sciences, School of Medicine and Public Health, University of Wisconsin - Madison, 610 Walnut St, WARF 707, Madison, WI 53726, USA.
| | - Ashley E Kates
- Division of Infectious Disease, Department of Medicine, School of Medicine and Public Health, University of Wisconsin - Madison, UW Med Fndtn Centennial Bldg, 1685 Highland Ave, Madison, WI 53705, USA; William S. Middleton Veterans Affairs Medical Center, 2500 Overlook Terrace, Madison, WI 53705, USA.
| | - Joseph H Skarlupka
- Department of Bacteriology, University of Wisconsin - Madison, 1550 Linden Dr, Madison, WI 53706, USA.
| | - Marty Kanarek
- Department of Population Health Sciences, School of Medicine and Public Health, University of Wisconsin - Madison, 610 Walnut St, WARF 707, Madison, WI 53726, USA; Nelson Institute for Environmental Studies, University of Wisconsin - Madison, 122 Science Hall, 550 North Park St, Madison, WI 53706, USA.
| | - Kristen M C Malecki
- Department of Population Health Sciences, School of Medicine and Public Health, University of Wisconsin - Madison, 610 Walnut St, WARF 707, Madison, WI 53726, USA.
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Salina EG, Grigorov A, Skvortsova Y, Majorov K, Bychenko O, Ostrik A, Logunova N, Ignatov D, Kaprelyants A, Apt A, Azhikina T. MTS1338, A Small Mycobacterium tuberculosis RNA, Regulates Transcriptional Shifts Consistent With Bacterial Adaptation for Entering Into Dormancy and Survival Within Host Macrophages. Front Cell Infect Microbiol 2019; 9:405. [PMID: 31850238 PMCID: PMC6901956 DOI: 10.3389/fcimb.2019.00405] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 11/12/2019] [Indexed: 11/13/2022] Open
Abstract
Small non-coding RNAs play a significant role in bacterial adaptation to changing environmental conditions. We investigated the dynamics of expression of MTS1338, a small non-coding RNA of Mycobacterium tuberculosis, in the mouse model in vivo, regulation of its expression in the infected macrophages, and the consequences of its overexpression in bacterial cultures. Here we demonstrate that MTS1338 significantly contributes to host-pathogen interactions. Activation of the host immune system triggered NO-inducible up-regulation of MTS1338 in macrophage-engulfed mycobacteria. Constitutive overexpression of MTS1338 in cultured mycobacteria improved their survival in vitro under low pH conditions. MTS1338 up-regulation launched a spectrum of shifts in the transcriptome profile similar to those reported for M. tuberculosis adaptation to hostile intra-macrophage environment. Using the RNA-seq approach, we demonstrate that gene expression changes accompanying MTS1338 overexpression indicate reduction in translational activity and bacterial growth. These changes indicate mycobacteria entering the dormant state. Taken together, our results suggest a direct involvement of this sRNA in the interplay between mycobacteria and the host immune system during infectious process.
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Affiliation(s)
- Elena G. Salina
- Laboratory of Biochemistry of Stresses in Microorganisms, Bach Institute of Biochemistry, Research Center of Biotechnology, Moscow, Russia
| | - Artem Grigorov
- Laboratory of Regulatory Transcriptomics, Department of Genomics and Postgenomic Technologies, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Yulia Skvortsova
- Laboratory of Regulatory Transcriptomics, Department of Genomics and Postgenomic Technologies, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Konstantin Majorov
- Laboratory for Immunogenetics, Department of Immunology, Central Institute for Tuberculosis, Moscow, Russia
| | - Oksana Bychenko
- Laboratory of Regulatory Transcriptomics, Department of Genomics and Postgenomic Technologies, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Albina Ostrik
- Laboratory of Biochemistry of Stresses in Microorganisms, Bach Institute of Biochemistry, Research Center of Biotechnology, Moscow, Russia
| | - Nadezhda Logunova
- Laboratory for Immunogenetics, Department of Immunology, Central Institute for Tuberculosis, Moscow, Russia
| | - Dmitriy Ignatov
- Laboratory of Regulatory Transcriptomics, Department of Genomics and Postgenomic Technologies, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Arseny Kaprelyants
- Laboratory of Biochemistry of Stresses in Microorganisms, Bach Institute of Biochemistry, Research Center of Biotechnology, Moscow, Russia
| | - Alexander Apt
- Laboratory for Immunogenetics, Department of Immunology, Central Institute for Tuberculosis, Moscow, Russia
| | - Tatyana Azhikina
- Laboratory of Regulatory Transcriptomics, Department of Genomics and Postgenomic Technologies, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
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Kim D, Ji S, Kim JR, Kim M, Byun JH, Yum JH, Yong D, Lee K. Performance evaluation of a new matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, ASTA MicroIDSys system, in bacterial identification against clinical isolates of anaerobic bacteria. Anaerobe 2019; 61:102131. [PMID: 31778809 DOI: 10.1016/j.anaerobe.2019.102131] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 11/15/2019] [Accepted: 11/23/2019] [Indexed: 12/21/2022]
Abstract
INTRODUCTION Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been introduced for bacterial identification. The ASTA MicroIDSys system (ASTA, Suwon, Korea) is a new MALDI-TOF MS system developed for species identification of microorganisms. We evaluated the performance of MicroIDSys against clinical isolates of anaerobic bacteria. MATERIAL AND METHODS A total of 370 non-duplicated clinical isolates of anaerobic bacteria were tested in this study. Bacterial identification with MicroIDSys was performed with a direct smear method, and measured spectra were analyzed using respective software. The results of MicroIDSys were compared with the results of Bruker Biotyper and 16S rRNA sequencing. RESULTS The overall agreement rates for the 370 clinical isolates (34 genera and 99 species) were 95.4% (353/370) at the genus level and 91.6% (n = 340) at the species level. Only 17 isolates were incorrectly identified at the genus level: five misidentifications and 12 unidentifications. The MicroIDSys system exhibited excellent performance in the identification of clinically relevant bacterial species. Most of the Bacteroides isolates (98.0%, 99/101) and all of the Clostridium difficile (100%, n = 11), Clostridium perfringens (100%, n = 10), Finegoldia magna (100%, n = 11), and Parvimonas micra (100%, n = 10) isolates were correctly identified at the species level. CONCLUSION The MicroIDSys system proved useful in the identification of anaerobic bacteria, especially clinically relevant species. This system could be of use in clinical microbiology laboratories as a primary tool for identifying anaerobic bacteria.
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Affiliation(s)
- Dokyun Kim
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University, College of Medicine, Seoul, South Korea
| | - Seungeun Ji
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University, College of Medicine, Seoul, South Korea
| | - Jung Rim Kim
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University, College of Medicine, Seoul, South Korea
| | - Myungsook Kim
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University, College of Medicine, Seoul, South Korea
| | - Jung-Hyun Byun
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University, College of Medicine, Seoul, South Korea
| | - Jong Hwa Yum
- Department of Clinical Laboratory Science, Dong-eui University, Busan, South Korea
| | - Dongeun Yong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University, College of Medicine, Seoul, South Korea
| | - Kyungwon Lee
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University, College of Medicine, Seoul, South Korea.
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Vadde KK, Feng Q, Wang J, McCarthy AJ, Sekar R. Next-generation sequencing reveals fecal contamination and potentially pathogenic bacteria in a major inflow river of Taihu Lake. Environ Pollut 2019; 254:113108. [PMID: 31491696 DOI: 10.1016/j.envpol.2019.113108] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 08/14/2019] [Accepted: 08/23/2019] [Indexed: 06/10/2023]
Abstract
Taihu Lake is one of the largest freshwater lakes in China and serves as an important source for drinking water. This lake is suffering from eutrophication, cyanobacterial blooms and fecal pollution, and the inflow Tiaoxi River is one of the main contributors. The goal here was to characterize the bacterial community structure of Tiaoxi River water by next-generation sequencing (NGS), paying attention to bacteria that are either fecal-associated or pathogenic, and to examine the relationship between environmental parameters and bacterial community structure. Water samples collected from 15 locations in three seasons, and fecal samples collected from different hosts and wastewater samples were used for bacterial community analysis. The phyla Proteobacteria, Actinobacteria, Bacteroidetes, and Cyanobacteria were predominant in most of the water samples tested. In fecal samples, Bacteroidetes, Firmicutes, and Proteobacteria were abundant, while wastewater samples were dominated by Proteobacteria, Bacteroidetes, Acidobacteria, and Chloroflexi. The cluster analysis and principal coordinate analysis indicated that bacterial community structure was significantly different between water, fecal and sewage samples. Shared OTUs between water samples and chicken, pig, and human fecal samples ranged from 4.5 to 9.8% indicating the presence of avian, pig and human fecal contamination in Tiaoxi River. At genus level, five bacterial genera of fecal origin and sequences of seven potential pathogens were detected in many locations and their presence was correlated well with the land use pattern. The sequencing data revealed that Faecalibacterium could be a potential target for human-associated microbial source-tracking qPCR assays. Our results suggest that pH, conductivity, and temperature were the main environmental factors in shaping the bacterial community based on redundancy analysis. Overall, NGS is a valuable tool for preliminary investigation of environmental samples to identify the potential human health risk, providing specific information about fecal and potentially pathogenic bacteria that can be followed up by specific methods.
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Affiliation(s)
- Kiran Kumar Vadde
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | - Qiaoli Feng
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | - Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Alan J McCarthy
- Microbiology Research Group, Institute of Integrative Biology, University of Liverpool, UK
| | - Raju Sekar
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, China.
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Romero-Lastra P, Sánchez MC, Llama-Palacios A, Figuero E, Herrera D, Sanz M. Gene expression of Porphyromonas gingivalis ATCC 33277 when growing in an in vitro multispecies biofilm. PLoS One 2019; 14:e0221234. [PMID: 31437202 PMCID: PMC6706054 DOI: 10.1371/journal.pone.0221234] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 08/01/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND AND OBJECTIVE Porphyromonas gingivalis, an oral microorganism residing in the subgingival biofilm, may exert diverse pathogenicity depending on the presence of specific virulence factors, but its gene expression has not been completely established. This investigation aims to compare the transcriptomic profile of this pathogen when growing within an in vitro multispecies biofilm or in a planktonic state. MATERIALS AND METHODS P. gingivalis ATCC 33277 was grown in anaerobiosis within multi-well culture plates at 37°C under two conditions: (a) planktonic samples (no hydroxyapatite discs) or (b) within a multispecies-biofilm containing Streptococcus oralis, Actinomyces naeslundii, Veillonella parvula, Fusobacterium nucleatum and Aggregatibacter actinomycetemcomitans deposited on hydroxyapatite discs. Scanning Electron Microscopy (SEM) and Confocal Laser Scanning Microscopy (CLSM) combined with Fluorescence In Situ Hybridization (FISH) were used to verify the formation of the biofilm and the presence of P. gingivalis. Total RNA was extracted from both the multispecies biofilm and planktonic samples, then purified and, with the use of a microarray, its differential gene expression was analyzed. A linear model was used for determining the differentially expressed genes using a filtering criterion of two-fold change (up or down) and a significance p-value of <0.05. Differential expression was confirmed by Reverse Transcription-quantitative Polymerase Chain Reaction (RT-qPCR). RESULTS SEM verified the development of the multispecies biofilm and FISH confirmed the incorporation of P. gingivalis. The microarray demonstrated that, when growing within the multispecies biofilm, 19.1% of P. gingivalis genes were significantly and differentially expressed (165 genes were up-regulated and 200 down-regulated), compared with planktonic growth. These genes were mainly involved in functions related to the oxidative stress, cell envelope, transposons and metabolism. The results of the microarray were confirmed by RT-qPCR. CONCLUSION Significant transcriptional changes occurred in P. gingivalis when growing in a multispecies biofilm compared to planktonic state.
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Affiliation(s)
- Patricia Romero-Lastra
- Laboratory of Dental Research, Faculty of Odontology, Complutense University of Madrid, Madrid, Spain
| | - María C. Sánchez
- Laboratory of Dental Research, Faculty of Odontology, Complutense University of Madrid, Madrid, Spain
- ETEP Research Group, Faculty of Odontology, Complutense University of Madrid, Madrid, Spain
| | - Arancha Llama-Palacios
- Laboratory of Dental Research, Faculty of Odontology, Complutense University of Madrid, Madrid, Spain
- ETEP Research Group, Faculty of Odontology, Complutense University of Madrid, Madrid, Spain
| | - Elena Figuero
- ETEP Research Group, Faculty of Odontology, Complutense University of Madrid, Madrid, Spain
- * E-mail:
| | - David Herrera
- ETEP Research Group, Faculty of Odontology, Complutense University of Madrid, Madrid, Spain
| | - Mariano Sanz
- ETEP Research Group, Faculty of Odontology, Complutense University of Madrid, Madrid, Spain
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Shi J, Feng Y. [New inhibitors targeting bacterial RNA polymerase]. Zhejiang Da Xue Xue Bao Yi Xue Ban 2019; 48:44-49. [PMID: 31102357 PMCID: PMC8800650 DOI: 10.3785/j.issn.1008-9292.2019.02.08] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 09/05/2018] [Indexed: 06/09/2023]
Abstract
Rifamycins, a group of bacterial RNA polymerase inhibitors, are the firstline antimicrobial drugs to treat tuberculosis. In light of the emergence of rifamycinresistant bacteria, development of new RNA polymerase inhibitors that kill rifamycinresistant bacteria with high bioavailability is urgent. Structural analysis of bacterial RNA polymerase in complex with inhibitors by crystallography and cryo-EM indicates that RNA polymerase inhibitors function through five distinct molecular mechanisms:inhibition of the extension of short RNA; competition with substrates; inhibition of the conformational change of the'bridge helix'; inhibition of clamp opening;inhibition of clamp closure. This article reviews the research progress of these five groups of RNA polymerase inhibitors to provide references for the modification of existing RNA polymerase inhibitors and the discovery of new RNA polymerase inhibitors.
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Affiliation(s)
- Jing Shi
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yu Feng
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou 310058, China
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
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Montoya DJ, Andrade P, Silva BJA, Teles RMB, Ma F, Bryson B, Sadanand S, Noel T, Lu J, Sarno E, Arnvig KB, Young D, Lahiri R, Williams DL, Fortune S, Bloom BR, Pellegrini M, Modlin RL. Dual RNA-Seq of Human Leprosy Lesions Identifies Bacterial Determinants Linked to Host Immune Response. Cell Rep 2019; 26:3574-3585.e3. [PMID: 30917313 PMCID: PMC6508871 DOI: 10.1016/j.celrep.2019.02.109] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 10/05/2018] [Accepted: 02/27/2019] [Indexed: 01/20/2023] Open
Abstract
To understand how the interaction between an intracellular bacterium and the host immune system contributes to outcome at the site of infection, we studied leprosy, a disease that forms a clinical spectrum, in which progressive infection by the intracellular bacterium Mycobacterium leprae is characterized by the production of type I IFNs and antibody production. Dual RNA-seq on patient lesions identifies two independent molecular measures of M. leprae, each of which correlates with distinct aspects of the host immune response. The fraction of bacterial transcripts, reflecting bacterial burden, correlates with a host type I IFN gene signature, known to inhibit antimicrobial responses. Second, the bacterial mRNA:rRNA ratio, reflecting bacterial viability, links bacterial heat shock proteins with the BAFF-BCMA host antibody response pathway. Our findings provide a platform for the interrogation of host and pathogen transcriptomes at the site of infection, allowing insight into mechanisms of inflammation in human disease.
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Affiliation(s)
- Dennis J Montoya
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Priscila Andrade
- Division of Dermatology, David Geffen School of Medicine, Los Angeles, CA, USA
| | - Bruno J A Silva
- Division of Dermatology, David Geffen School of Medicine, Los Angeles, CA, USA
| | - Rosane M B Teles
- Division of Dermatology, David Geffen School of Medicine, Los Angeles, CA, USA
| | - Feiyang Ma
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Bryan Bryson
- Harvard T.H. Chan School of Public Health, Department of Immunology and Infectious Diseases, Boston, MA, USA
| | | | - Teia Noel
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Jing Lu
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Euzenir Sarno
- Department of Mycobacteriosis, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Kristine B Arnvig
- Institute for Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - Douglas Young
- National Institute for Medical Research, Mycobacterial Research Division, London NW7 1AA, UK; The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Ramanuj Lahiri
- Health Resources and Services Administration (HRSA), National Hansen's Disease Program (NHDP), Baton Rouge, LA, USA
| | - Diana L Williams
- Health Resources and Services Administration (HRSA), National Hansen's Disease Program (NHDP), Baton Rouge, LA, USA; Department of Pathobiological Sciences, Louisiana State University (LSU), Baton Rouge, LA, USA
| | - Sarah Fortune
- Harvard T.H. Chan School of Public Health, Department of Immunology and Infectious Diseases, Boston, MA, USA
| | - Barry R Bloom
- Harvard T.H. Chan School of Public Health, Department of Immunology and Infectious Diseases, Boston, MA, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Robert L Modlin
- Division of Dermatology, David Geffen School of Medicine, Los Angeles, CA, USA.
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Song M, Luo C, Jiang L, Peng K, Zhang D, Zhang R, Li Y, Zhang G. The presence of in situ sulphamethoxazole degraders and their interactions with other microbes in activated sludge as revealed by DNA stable isotope probing and molecular ecological network analysis. Environ Int 2019; 124:121-129. [PMID: 30641255 DOI: 10.1016/j.envint.2018.12.039] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 12/15/2018] [Accepted: 12/17/2018] [Indexed: 06/09/2023]
Abstract
Wastewater treatment plants (WWTPs) are the main hotspots for the release of antibiotics, including the widely used sulphonamides. Microbes play important roles in eliminating sulphonamides in WWTPs, and knowledge about these degraders and their interactions within the microbial community is crucial for operating and optimising WWTPs. In the present study, stable isotope probing (SIP) coupled with high-throughput sequencing as culture-independent approach revealed four operational taxonomic units (OTUs) involved in sulphamethoxazole (SMX) degradation in activated sludge. Except for the OTU affiliated with Gammaproteobacteria, the others have not been previously reported to possess the ability to metabolise SMX. The isolated SMX degrader by culture-dependent method did not participate in SMX biodegradation in situ according to the SIP analysis, and showed weak correlations with other members in the activated sludge. The complex interactions between in situ active SMX degraders and non-degrading microbes might explain our failure to isolate these degraders. In addition, sul1 genes associated with SMX resistance were also labelled with 13C, suggesting that they might benefit from SMX degradation and/or originate from the active SMX degraders. These findings broaden our understanding of the diversity of SMX-degrading microbes and their associated characteristics in WWTPs.
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Affiliation(s)
- Mengke Song
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; Joint Institute for Environmental Research and Education, South China Agricultural University, Guangzhou 510642, China
| | - Chunling Luo
- Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; Joint Institute for Environmental Research and Education, South China Agricultural University, Guangzhou 510642, China.
| | - Longfei Jiang
- Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Ke Peng
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Dayi Zhang
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Ruijie Zhang
- School of Marine Sciences, Guangxi University, Nanning 530004, China
| | - Yongtao Li
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; Joint Institute for Environmental Research and Education, South China Agricultural University, Guangzhou 510642, China
| | - Gan Zhang
- Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
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Yang ZJ, Concilio MG, Ramesh V, Zhang LH. Synthesis and Evaluation of Novel Neamine-Nucleoside Conjugates as Potential Antibiotic Targets for Escherichia coli 16S Ribosomal RNA. Methods Mol Biol 2019; 1870:151-163. [PMID: 30539553 DOI: 10.1007/978-1-4939-8808-2_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Based on the nucleobase rich character of the binding pocket of A-site 16S ribosomal RNA of Escherichia coli, it was proposed that the neamine moiety of synthesized Neamine-nucleoside conjugates could bind to the groove of RNA while the nucleobase moiety would bind specifically to the sequence of the 16S rRNA A-site fragment. Thus the designed conjugate compound 5 was found to have the same dissociation constant as neamine for binding to 16S rRNA and the neamine-amino acid substituted nucleoside conjugate 8 and 9 showed 6.3 and 4.8 times greater RNA binding affinity, respectively, as compared with neamine. The results obtained successfully demonstrate the need for chemically modifying neamine and probe the changes induced using NMR protocols to assist in the discovery of new aminoglycoside antibiotics.
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Affiliation(s)
- Zhen-Jun Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | | | | | - Li-He Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China.
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Arya S, Dubey V, Sen D, Sharma A, Pathania R. Computational Prediction of sRNA in Acinetobacter baumannii. Methods Mol Biol 2019; 1946:307-320. [PMID: 30798565 DOI: 10.1007/978-1-4939-9118-1_27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Small RNAs in bacteria are noncoding RNAs that act as posttranscriptional regulators of gene expression. Over time, they have gained importance as fine-tuners of expression of genes involved in critical biological processes like metabolism, fitness, virulence, and antibiotic resistance. The availability of various high-throughput strategies enable the detection of these molecules but are technically challenging and time-intensive. Thus, to fulfil the need of a simple computational algorithm pipeline to predict these sRNAs in bacterial species, we detail a user-friendly ensemble method with specific application in Acinetobacter spp. The developed algorithms primarily look for intergenic regions in the genome of related Acinetobacter spp., thermodynamic stability, and conservation of RNA secondary structures to generate a model input for the sRNAPredict3 tool which utilizes all this information to generate a list of putative sRNA. We confirmed the accuracy of the method by comparing its output with the RNA-seq data and found the method to be faster and more accurate for Acinetobacter baumannii ATCC 17978. Thus, this method improves the identification of sRNA in Acinetobacter and other bacterial species.
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Affiliation(s)
- Sankalp Arya
- Department of Biotechnology, Indian Institute of Technology-Roorkee, Roorkee, Uttarakhand, India
- Division of Agricultural and Environmental Sciences, University of Nottingham, Nottingham, UK
| | - Vineet Dubey
- Department of Biotechnology, Indian Institute of Technology-Roorkee, Roorkee, Uttarakhand, India
| | - Deepak Sen
- Department of Biotechnology, Indian Institute of Technology-Roorkee, Roorkee, Uttarakhand, India
| | - Atin Sharma
- Department of Biotechnology, Indian Institute of Technology-Roorkee, Roorkee, Uttarakhand, India
| | - Ranjana Pathania
- Department of Biotechnology, Indian Institute of Technology-Roorkee, Roorkee, Uttarakhand, India.
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Fuirst M, Veit RR, Hahn M, Dheilly N, Thorne LH. Effects of urbanization on the foraging ecology and microbiota of the generalist seabird Larus argentatus. PLoS One 2018; 13:e0209200. [PMID: 30562368 PMCID: PMC6298667 DOI: 10.1371/journal.pone.0209200] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 12/01/2018] [Indexed: 01/22/2023] Open
Abstract
Larus gull species have proven adaptable to urbanization and due to their generalist feeding behaviors, they provide useful opportunities to study how urban environments impact foraging behavior and host-associated microbiota. We evaluated how urbanization influenced the foraging behavior and microbiome characteristics of breeding herring gulls (Larus argentatus) at three different colonies on the east coast of the United States. Study colonies represented high, medium and low degrees of urbanization, respectively. At all colonies, gulls frequently foraged at landfills and in other urban environments, but both the use of urban environments and gull foraging metrics differed with the degree of urbanization. Gulls at the more urban colonies used urban environments more frequently, showed higher rates of site fidelity and took shorter trips. Gulls at less urban colonies used a greater diversity of habitat types and foraged offshore. We observed high microbial diversity at all colonies, though microbial diversity was highest at the least urban colony where gulls used a wider variety of foraging habitats. This suggests that gulls may acquire a wider range of bacteria when visiting a higher variety of foraging sites. Our findings highlight the influence of urban habitats on gull movements and microbiome composition and diversity during the breeding season and represent the first application of amplicon sequence variants, an objective and repeatable method of bacterial classification, to study the microbiota of a seabird species.
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Affiliation(s)
- Matthew Fuirst
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, United States of America
| | - Richard R. Veit
- Department of Biology, College of Staten Island (CSI) CUNY, Staten Island, NY, United States of America
| | - Megan Hahn
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, United States of America
| | - Nolwenn Dheilly
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, United States of America
| | - Lesley H. Thorne
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, United States of America
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Raut S, Polley HW, Fay PA, Kang S. Bacterial community response to a preindustrial-to-future CO 2 gradient is limited and soil specific in Texas Prairie grassland. Glob Chang Biol 2018; 24:5815-5827. [PMID: 30230661 DOI: 10.1111/gcb.14453] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 09/07/2018] [Indexed: 06/08/2023]
Abstract
Rising atmospheric CO2 concentration directly stimulates plant productivity and affects nutrient dynamics in the soil. However, the influence of CO2 enrichment on soil bacterial communities remains elusive, likely due to their complex interactions with a wide range of plant and soil properties. Here, we investigated the bacterial community response to a decade long preindustrial-to-future CO2 gradient (250-500 ppm) among three contrasting soil types using 16S rRNA gene amplicon sequencing. In addition, we examined the effect of seasonal variation and plant species composition on bacterial communities. We found that Shannon index (H') and Faith's phylogenetic diversity (PD) did not change in response to the CO2 gradient (R2 = 0.01, p > 0.05). CO2 gradient and season also had a negligible effect on overall community structure, although silty clay soil communities were better structured on a CO2 gradient (p < 0.001) among three soils. Similarly, CO2 gradient had no significant effect on the relative abundance of different phyla. However, we observed soil-specific variation of CO2 effects in a few individual families. For example, the abundance of Pirellulaceae family decreased linearly with CO2 gradient, but only in sandy loam soils. Conversely, the abundance of Micromonosporaceae and Gaillaceae families increased with CO2 gradient in clay soils. Soil water content (SWC) and nutrient properties were the key environmental constraints shaping bacterial community structure, one manifestation of which was a decline in bacterial diversity with increasing SWC. Furthermore, the impact of plant species composition on community structure was secondary to the strong influence of soil properties. Taken together, our findings indicate that bacterial communities may be largely unresponsive to indirect effects of CO2 enrichment through plants. Instead, bacterial communities are strongly regulated by edaphic conditions, presumably because soil differences create distinct environmental niches for bacteria.
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Affiliation(s)
- Swastika Raut
- Department of Biology, Baylor University, Waco, Texas
| | - Herbert W Polley
- Grassland, Soil and Water Research Laboratory, Department of Agriculture, Agricultural Research Service, Temple, Texas
| | - Philip A Fay
- Grassland, Soil and Water Research Laboratory, Department of Agriculture, Agricultural Research Service, Temple, Texas
| | - Sanghoon Kang
- Department of Biology, Baylor University, Waco, Texas
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Compo NR, Gomez DE, Tapscott B, Weese JS, Turner PV. Fecal bacterial microbiota of Canadian commercial mink (Neovison vison): Yearly, life stage, and seasonal comparisons. PLoS One 2018; 13:e0207111. [PMID: 30419047 PMCID: PMC6231641 DOI: 10.1371/journal.pone.0207111] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 10/25/2018] [Indexed: 01/01/2023] Open
Abstract
The gastrointestinal microbiome is known to play a critical role in animal health but has been relatively poorly characterized in commercial mink, an obligate carnivore. Whether the microbiota can be manipulated in mink to improve pelt quality, health, and well-being is unknown. The objectives of this study were to characterize the fecal microbiota of commercial mink, and to evaluate potential changes due to year (2014 vs 2015), life stage (adult female vs weaned kit), season (summer vs winter), and between Canadian farms. Pooled fecal samples were collected from adult females and weaned kits in the summers of 2014 (n = 173) and 2015 (n = 168), and from females in the winter of 2016 (n = 39), a time when females undergo marked calorie restriction, from 49 mink farms in Ontario. Bacterial DNA was extracted and the V4 region of the 16S rRNA gene was amplified. Approximately 22 million sequences were identified following quality control filtering. A total of 31 bacterial phyla were identified; however, only 3 comprised >1% of the total sequences identified, with Firmicutes and Proteobacteria together comprising 95% of the total sequences. Comparisons were made by life stage, season and year; no differences were found in the relative abundance of any taxa between samples collected from adult females and weaned kits from the same year and the greatest number of differences at each taxonomic level were noted between 2014 and 2015. Significantly more operational taxonomic units (OTUs) were found in 2014 than 2015 or 2016 (p<0.05) and samples from 2014 were more even, but less diverse than in 2015 (p = 0.002 and 0.001, respectively). There were significant differences in community population and structure by year and season (all p-values <0.001). The predominant phyla and genera at the farm level were similar from year to year. Together, these indicate that mink environment, season, and time are important factors in the stability of gastrointestinal microbiota, once mink reach maturity.
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Affiliation(s)
- Nicole R. Compo
- Department of Pathobiology, University of Guelph, Guelph, Ontario, Canada
| | - Diego E. Gomez
- Department of Pathobiology, University of Guelph, Guelph, Ontario, Canada
| | - Brian Tapscott
- Ontario Ministry of Agriculture, Food, and Rural Affairs, Elora, Ontario, Canada
| | - J. Scott Weese
- Department of Pathobiology, University of Guelph, Guelph, Ontario, Canada
| | - Patricia V. Turner
- Department of Pathobiology, University of Guelph, Guelph, Ontario, Canada
- * E-mail:
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Abstract
BACKGROUND Small RNAs (sRNAs) are noncoding molecules that regulate different cellular activities in several bacteria. The role of sRNAs in gene expression regulation is poorly characterized in the etiological agent of porcine enzootic pneumonia Mycoplasma hyopneumoniae. We performed a global analysis of the sRNAs, sRNA target genes and regulatory elements previously identified in their genome and analyzed the expression of some sRNAs and their target genes by quantitative RT-PCR (qPCR) in three different culture conditions. RESULTS Seven of the 145 sRNA target genes are organized as monocistronic genes (mCs) while the other 138 sRNA target genes are organized into transcriptional units (TU). The identification of transcriptional regulatory elements (promoter motif, DNA repeat sequence or intrinsic terminator) was verified in 116 of the 145 sRNA target genes. Moreover, the 29 sRNA target genes without regulatory elements revealed the presence of at least one regulatory element in the boundaries of the TU or in other internal genes of the TU. We verified that 16 sRNAs showed differential expression, seven in heat shock condition and 14 in oxidative stress condition. Analysis of the differential expression of the sRNA target genes showed that the tested sRNAs possibly regulate gene expression. The sRNA target genes were up- or down-regulated possibly in response to sRNA only under oxidative stress condition. Moreover, the sRNA target genes are involved in diverse processes of the cell, some of which could be linked to transcription processes and cell homeostasis. CONCLUSION Our results indicate that bacterial sRNAs could regulate a number of targets with various outcomes, and different correlations between the levels of sRNA transcripts and their target gene mRNAs were found, which suggest that the regulation of gene expression via sRNAs may play an important role in mycoplasma.
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Affiliation(s)
- Tiago Ebert Fritsch
- Centro de Biotecnologia, Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS Brazil
| | - Franciele Maboni Siqueira
- Centro de Biotecnologia, Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS Brazil
| | - Irene Silveira Schrank
- Centro de Biotecnologia, Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS Brazil
- Departamento de Biologia Molecular e Biotecnologia – Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves 9500, P. 43421, C.P. 15005, CEP, Porto Alegre, RS 91501-970 Brazil
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Cortez V, Canal E, Dupont-Turkowsky JC, Quevedo T, Albujar C, Chang TC, Salmon-Mulanovich G, Guezala-Villavicencio MC, Simons MP, Margolis E, Schultz-Cherry S, Pacheco V, Bausch DG. Identification of Leptospira and Bartonella among rodents collected across a habitat disturbance gradient along the Inter-Oceanic Highway in the southern Amazon Basin of Peru. PLoS One 2018; 13:e0205068. [PMID: 30300359 PMCID: PMC6177132 DOI: 10.1371/journal.pone.0205068] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 09/18/2018] [Indexed: 11/19/2022] Open
Abstract
Background The southern Amazon Basin in the Madre de Dios region of Peru has undergone rapid deforestation and habitat disruption, leading to an unknown zoonotic risk to the growing communities in the area. Methodology/Principal findings We surveyed the prevalence of rodent-borne Leptospira and Bartonella, as well as potential environmental sources of human exposure to Leptospira, in 4 communities along the Inter-Oceanic Highway in Madre de Dios. During the rainy and dry seasons of 2014–2015, we captured a total of 97 rodents representing 8 genera in areas that had experienced different degrees of habitat disturbance. Primarily by using 16S metagenomic sequencing, we found that most of the rodents (78%) tested positive for Bartonella, whereas 24% were positive for Leptospira; however, the patterns differed across seasons and the extent of habitat disruption. A high prevalence of Bartonella was identified in animals captured across both trapping seasons (72%–83%) and the relative abundance was correlated with increasing level of land disturbance. Leptospira-positive animals were more than twice as prevalent during the rainy season (37%) as during the dry season (14%). A seasonal fluctuation across the rainy, dry, and mid seasons was also apparent in environmental samples tested for Leptospira (range, 55%–89% of samples testing positive), and there was a high prevalence of this bacteria across all sites that were sampled in the communities. Conclusions/Significance These data indicate the need for increased awareness of rodent-borne disease and the potential for environmental spread along the communities in areas undergoing significant land-use change.
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Affiliation(s)
- Valerie Cortez
- U.S. Naval Medical Research Unit No. 6, Callao, Peru
- St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
- * E-mail:
| | - Enrique Canal
- U.S. Naval Medical Research Unit No. 6, Callao, Peru
| | | | | | | | - Ti-Cheng Chang
- St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Gabriela Salmon-Mulanovich
- U.S. Naval Medical Research Unit No. 6, Callao, Peru
- Pontificia Universidad Católica del Peru, Lima, Peru
| | | | | | - Elisa Margolis
- St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | | | - Víctor Pacheco
- Universidad Nacional Mayor de San Marcos, Museo de Historia Natural, Lima, Peru
| | - Daniel G. Bausch
- U.S. Naval Medical Research Unit No. 6, Callao, Peru
- Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana, United States of America
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Sarin LP, Kienast SD, Leufken J, Ross RL, Dziergowska A, Debiec K, Sochacka E, Limbach PA, Fufezan C, Drexler HCA, Leidel SA. Nano LC-MS using capillary columns enables accurate quantification of modified ribonucleosides at low femtomol levels. RNA 2018; 24:1403-1417. [PMID: 30012570 PMCID: PMC6140458 DOI: 10.1261/rna.065482.117] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 07/11/2018] [Indexed: 05/14/2023]
Abstract
Post-transcriptional chemical modifications of (t)RNA molecules are crucial in fundamental biological processes, such as translation. Despite their biological importance and accumulating evidence linking them to various human diseases, technical challenges have limited their detection and accurate quantification. Here, we present a sensitive capillary nanoflow liquid chromatography mass spectrometry (nLC-MS) pipeline for quantitative high-resolution analysis of ribonucleoside modifications from complex biological samples. We evaluated two porous graphitic carbon (PGC) materials and one end-capped C18 reference material as stationary phases for reversed-phase separation. We found that these matrices have complementing retention and separation characteristics, including the capability to separate structural isomers. PGC and C18 matrices yielded excellent signal-to-noise ratios in nLC-MS while differing in the separation capability and sensitivity for various nucleosides. This emphasizes the need for tailored LC-MS setups for optimally detecting as many nucleoside modifications as possible. Detection ranges spanning up to six orders of magnitude enable the analysis of individual ribonucleosides down to femtomol concentrations. Furthermore, normalizing the obtained signal intensities to a stable isotope labeled spike-in enabled direct comparison of ribonucleoside levels between different samples. In conclusion, capillary columns coupled to nLC-MS constitute a powerful and sensitive tool for quantitative analysis of modified ribonucleosides in complex biological samples. This setup will be invaluable for further unraveling the intriguing and multifaceted biological roles of RNA modifications.
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Affiliation(s)
- L Peter Sarin
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Muenster, 48149, Germany
- Cells-in-Motion Cluster of Excellence, University of Muenster, Muenster, 48149, Germany
| | - Sandra D Kienast
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Muenster, 48149, Germany
- Cells-in-Motion Cluster of Excellence, University of Muenster, Muenster, 48149, Germany
| | - Johannes Leufken
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Muenster, 48149, Germany
- Cells-in-Motion Cluster of Excellence, University of Muenster, Muenster, 48149, Germany
| | - Robert L Ross
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221-0172, USA
| | - Agnieszka Dziergowska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, 90-924 Lodz, Poland
| | - Katarzyna Debiec
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, 90-924 Lodz, Poland
| | - Elzbieta Sochacka
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, 90-924 Lodz, Poland
| | - Patrick A Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221-0172, USA
| | - Christian Fufezan
- Institute of Plant Biology and Biotechnology, University of Muenster, Muenster, 48143, Germany
| | - Hannes C A Drexler
- Bioanalytical Mass Spectrometry Unit, Max Planck Institute for Molecular Biomedicine, Muenster, 48149, Germany
| | - Sebastian A Leidel
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Muenster, 48149, Germany
- Cells-in-Motion Cluster of Excellence, University of Muenster, Muenster, 48149, Germany
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50
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Huang H, Zhao Y, Xu Z, Ding Y, Zhang W, Wu L. Biosorption characteristics of a highly Mn(II)-resistant Ralstonia pickettii strain isolated from Mn ore. PLoS One 2018; 13:e0203285. [PMID: 30169522 PMCID: PMC6118360 DOI: 10.1371/journal.pone.0203285] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 08/19/2018] [Indexed: 11/25/2022] Open
Abstract
Microorganisms play an important role in immobilizing and detoxifying excessive Mn; however, there is so far a lack of sufficient information concerning highly Mn(II)-tolerant bacteria. The present study was conducted to analyze the bio-sorption characteristics of a strain (HM8) isolated from manganese ore wastes. Analytical data from the 16S rDNA sequence determination showed that the species, HM8, had a 99% similarity to Ralstonia pickettii. Results from the designed physiological, biochemical and isothermal adsorption tests indicated that HM8 did not only grow well at a Mn(II) concentration level of 10,000 mg/L but also removed 1,002.83 mg/L of Mn(II) from the bulk solution of the culture, showing that the isolated strain possessed strong capabilities to tolerate and remove Mn(II). In the isothermal bio-sorption experiments performed to investigate the effects of relevant factors on Mn(II) sorption, the highest Mn(II) removal rate was obtained at the contact time 72 h, temperature 40°C, and pH 6.0, while the differences in both strain growth and Mn(II) removal rate between different inoculated HM8 doses were found to be insignificant within the tested range. Scanning electron microscopy showed that, under Mn(II) stress, HM8 cells appeared irregular and cracked, with apparent wrinkles on the surface. The peaks in the Fourier transform infrared spectra showed that hydroxyl and carboxyl groups were the main functional groups for Mn(II) adsorption. The experimental data supported the practical application of HM8 as a biological adsorbent for remediation of heavily Mn contaminated sites.
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Affiliation(s)
- Huimin Huang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Yunlin Zhao
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Zhenggang Xu
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, Hunan, China
- School of Material and Chemical Engineering, Hunan City University, Yiyang, Hunan, China
- * E-mail:
| | - Yi Ding
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Wan Zhang
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Liang Wu
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, Hunan, China
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