1
|
Žedaveinytė R, Meers C, Le HC, Mortman EE, Tang S, Lampe GD, Pesari SR, Gelsinger DR, Wiegand T, Sternberg SH. Antagonistic conflict between transposon-encoded introns and guide RNAs. Science 2024; 385:eadm8189. [PMID: 38991068 DOI: 10.1126/science.adm8189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 05/08/2024] [Indexed: 07/13/2024]
Abstract
TnpB nucleases represent the evolutionary precursors to CRISPR-Cas12 and are widespread in all domains of life. IS605-family TnpB homologs function as programmable RNA-guided homing endonucleases in bacteria, driving transposon maintenance through DNA double-strand break-stimulated homologous recombination. In this work, we uncovered molecular mechanisms of the transposition life cycle of IS607-family elements that, notably, also encode group I introns. We identified specific features for a candidate "IStron" from Clostridium botulinum that allow the element to carefully control the relative levels of spliced products versus functional guide RNAs. Our results suggest that IStron transcripts evolved an ability to balance competing and mutually exclusive activities that promote selfish transposon spread while limiting adverse fitness costs on the host. Collectively, this work highlights molecular innovation in the multifunctional utility of transposon-encoded noncoding RNAs.
Collapse
Affiliation(s)
- Rimantė Žedaveinytė
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Chance Meers
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Hoang C Le
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Edan E Mortman
- Department of Genetics and Development, Columbia University, New York, NY 10032, USA
| | - Stephen Tang
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - George D Lampe
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Sanjana R Pesari
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Diego R Gelsinger
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Tanner Wiegand
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Samuel H Sternberg
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| |
Collapse
|
2
|
Kochanowsky R, Carothers K, Roxas BAP, Anwar F, Viswanathan VK, Vedantam G. Clostridioides difficile superoxide reductase mitigates oxygen sensitivity. J Bacteriol 2024:e0017524. [PMID: 38953644 DOI: 10.1128/jb.00175-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 06/12/2024] [Indexed: 07/04/2024] Open
Abstract
Clostridioides difficile causes a serious diarrheal disease and is a common healthcare-associated bacterial pathogen. Although it has a major impact on human health, the mechanistic details of C. difficile intestinal colonization remain undefined. C. difficile is highly sensitive to oxygen and requires anaerobic conditions for in vitro growth. However, the mammalian gut is not devoid of oxygen, and C. difficile tolerates moderate oxidative stress in vivo. The C. difficile genome encodes several antioxidant proteins, including a predicted superoxide reductase (SOR) that is upregulated upon exposure to antimicrobial peptides. The goal of this study was to establish SOR enzymatic activity and assess its role in protecting C. difficile against oxygen exposure. Insertional inactivation of sor rendered C. difficile more sensitive to superoxide, indicating that SOR contributes to antioxidant defense. Heterologous C. difficile sor expression in Escherichia coli conferred protection against superoxide-dependent growth inhibition, and the corresponding cell lysates showed superoxide scavenging activity. Finally, a C. difficile SOR mutant exhibited global proteome changes under oxygen stress when compared to the parent strain. Collectively, our data establish the enzymatic activity of C. difficile SOR, confirm its role in protection against oxidative stress, and demonstrate SOR's broader impacts on the C. difficile vegetative cell proteome.IMPORTANCEClostridioides difficile is an important pathogen strongly associated with healthcare settings and capable of causing severe diarrheal disease. While considered a strict anaerobe in vitro, C. difficile has been shown to tolerate low levels of oxygen in the mammalian host. Among other well-characterized antioxidant proteins, the C. difficile genome encodes a predicted superoxide reductase (SOR), an understudied component of antioxidant defense in pathogens. The significance of the research reported herein is the characterization of SOR's enzymatic activity, including confirmation of its role in protecting C. difficile against oxidative stress. This furthers our understanding of C. difficile pathogenesis and presents a potential new avenue for targeted therapies.
Collapse
Affiliation(s)
- Rebecca Kochanowsky
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, USA
| | - Katelyn Carothers
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, USA
| | - Bryan Angelo P Roxas
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, USA
| | - Farhan Anwar
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, USA
| | - V K Viswanathan
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, USA
- BIO5 Institute for Collaborative Research, The University of Arizona, Tucson, Arizona, USA
| | - Gayatri Vedantam
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, USA
- BIO5 Institute for Collaborative Research, The University of Arizona, Tucson, Arizona, USA
- Southern Arizona VA Healthcare System, Tucson, Arizona, USA
| |
Collapse
|
3
|
Troitzsch D, Knop R, Dittmann S, Bartel J, Zühlke D, Möller TA, Trän L, Echelmeyer T, Sievers S. Characterizing the flavodoxin landscape in Clostridioides difficile. Microbiol Spectr 2024; 12:e0189523. [PMID: 38319052 PMCID: PMC10913485 DOI: 10.1128/spectrum.01895-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 12/23/2023] [Indexed: 02/07/2024] Open
Abstract
Clostridioides difficile infections have become a major challenge in medical facilities. The bacterium is capable of spore formation allowing the survival of antibiotic treatment. Therefore, research on the physiology of C. difficile is important for the development of alternative treatment strategies. In this study, we investigated eight putative flavodoxins of C. difficile 630. Flavodoxins are small electron transfer proteins of specifically low potential. The unusually high number of flavodoxins in C. difficile suggests that they are expressed under different conditions. We determined high transcription levels for several flavodoxins during the exponential growth phase, especially for floX. Since flavodoxins are capable of replacing ferredoxins under iron deficiency conditions in other bacteria, we also examined their expression in C. difficile under low iron and no iron levels. In particular, the amount of fldX increased with decreasing iron concentration and thus could possibly replace ferredoxins. Moreover, we demonstrated that fldX is increasingly expressed under different oxidative stress conditions and thus may play an important role in the oxidative stress response. While increased fldX expression was detectable at both RNA and protein level, CD2825 showed increased expression only at mRNA level under H2O2 stress with sufficient iron availability and may indicate hydroxyl radical-dependent transcription. Although the exact function of the individual flavodoxins in C. difficile needs to be further investigated, the present study shows that flavodoxins could play an important role in several physiological processes and under infection-relevant conditions. IMPORTANCE The gram-positive, anaerobic, and spore-forming bacterium Clostridioides difficile has become a vast problem in human health care facilities. The antibiotic-associated infection with this intestinal pathogen causes serious and recurrent inflammation of the intestinal epithelium, in many cases with a severe course. To come up with novel targeted therapies against C. difficile infections, a more detailed knowledge on the pathogen's physiology is mandatory. Eight putative flavodoxins, an extraordinarily high copy number of this type of small electron transfer proteins, are annotated for C. difficile. Flavodoxins are known to be essential electron carriers in other bacteria, for instance, during infection-relevant conditions such as iron limitation and oxidative stress. This work is a first and comprehensive overview on characteristics and expression profiles of the putative flavodoxins in the pathogen C. difficile.
Collapse
Affiliation(s)
- Daniel Troitzsch
- Department of Microbial Physiology and Molecular Biology, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Robert Knop
- Department of Microbial Physiology and Molecular Biology, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Silvia Dittmann
- Department of Microbial Physiology and Molecular Biology, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Jürgen Bartel
- Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Daniela Zühlke
- Department of Microbial Physiology and Molecular Biology, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Timon Alexander Möller
- Department of Microbial Physiology and Molecular Biology, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Linda Trän
- Department of Microbial Physiology and Molecular Biology, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Thaddäus Echelmeyer
- Department of Microbial Physiology and Molecular Biology, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Susanne Sievers
- Department of Microbial Physiology and Molecular Biology, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| |
Collapse
|
4
|
Smith AB, Specker JT, Hewlett KK, Scoggins TR, Knight M, Lustig AM, Li Y, Evans KM, Guo Y, She Q, Christopher MW, Garrett TJ, Moustafa AM, Van Tyne D, Prentice BM, Zackular JP. Liberation of host heme by Clostridioides difficile-mediated damage enhances Enterococcus faecalis fitness during infection. mBio 2024; 15:e0165623. [PMID: 38078767 PMCID: PMC10790701 DOI: 10.1128/mbio.01656-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 10/23/2023] [Indexed: 01/17/2024] Open
Abstract
IMPORTANCE Clostridioides difficile and Enterococcus faecalis are two pathogens of great public health importance. Both bacteria colonize the human gastrointestinal tract where they are known to interact in ways that worsen disease outcomes. We show that the damage associated with C. difficile infection (CDI) releases nutrients that benefit E. faecalis. One particular nutrient, heme, allows E. faecalis to use oxygen to generate energy and grow better in the gut. Understanding the mechanisms of these interspecies interactions could inform therapeutic strategies for CDI.
Collapse
Affiliation(s)
- Alexander B. Smith
- Division of Protective Immunity, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | - Katharine K. Hewlett
- Division of Protective Immunity, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Troy R. Scoggins
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Montana Knight
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Abigail M. Lustig
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yanhong Li
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Tsinghua University School of Medicine, Beijing, China
| | - Kirsten M. Evans
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yingchan Guo
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Qianxuan She
- Division of Protective Immunity, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | - Timothy J. Garrett
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, Florida, USA
| | - Ahmed M. Moustafa
- Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Daria Van Tyne
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Boone M. Prentice
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Joseph P. Zackular
- Division of Protective Immunity, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| |
Collapse
|
5
|
Hastie JL, Carmichael HL, Werner BM, Dunbar KE, Carlson PE. Clostridioides difficile utilizes siderophores as an iron source and FhuDBGC contributes to ferrichrome uptake. J Bacteriol 2023; 205:e0032423. [PMID: 37971230 PMCID: PMC10729759 DOI: 10.1128/jb.00324-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 10/26/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE This study is the first example of C. difficile growing with siderophores as the sole iron source and describes the characterization of the ferric hydroxamate uptake ABC transporter (FhuDBGC). This transporter shows specificity to the siderophore ferrichrome. While not required for pathogenesis, this transporter highlights the redundancy in iron acquisition mechanisms that C. difficile uses to compete for iron during an infection.
Collapse
Affiliation(s)
- Jessica L. Hastie
- Food and Drug Administration, Center for Biologics Evaluation and Research, Office of Vaccines Research and Review, Division of Bacterial Parasitic and Allergenic Products, Laboratory of Mucosal Pathogens and Cellular Immunology, Silver Spring, Maryland, USA
| | - Hannah L. Carmichael
- Food and Drug Administration, Center for Biologics Evaluation and Research, Office of Vaccines Research and Review, Division of Bacterial Parasitic and Allergenic Products, Laboratory of Mucosal Pathogens and Cellular Immunology, Silver Spring, Maryland, USA
| | - Bailey M. Werner
- Food and Drug Administration, Center for Biologics Evaluation and Research, Office of Vaccines Research and Review, Division of Bacterial Parasitic and Allergenic Products, Laboratory of Mucosal Pathogens and Cellular Immunology, Silver Spring, Maryland, USA
| | - Kristin E. Dunbar
- Food and Drug Administration, Center for Biologics Evaluation and Research, Office of Vaccines Research and Review, Division of Bacterial Parasitic and Allergenic Products, Laboratory of Mucosal Pathogens and Cellular Immunology, Silver Spring, Maryland, USA
| | - Paul E. Carlson
- Food and Drug Administration, Center for Biologics Evaluation and Research, Office of Vaccines Research and Review, Division of Bacterial Parasitic and Allergenic Products, Laboratory of Mucosal Pathogens and Cellular Immunology, Silver Spring, Maryland, USA
| |
Collapse
|
6
|
Žedaveinytė R, Meers C, Le HC, Mortman EE, Tang S, Lampe GD, Pesari SR, Gelsinger DR, Wiegand T, Sternberg SH. Antagonistic conflict between transposon-encoded introns and guide RNAs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.20.567912. [PMID: 38045383 PMCID: PMC10690162 DOI: 10.1101/2023.11.20.567912] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
TnpB nucleases represent the evolutionary precursors to CRISPR-Cas12 and are widespread in all domains of life, presumably due to the critical roles they play in transposon proliferation. IS605family TnpB homologs function in bacteria as programmable homing endonucleases by exploiting transposon-encoded guide RNAs to cleave vacant genomic sites, thereby driving transposon maintenance through DSB-stimulated homologous recombination. Whether this pathway is conserved in other genetic contexts, and in association with other transposases, is unknown. Here we uncover molecular mechanisms of transposition and RNA-guided DNA cleavage by IS607-family elements that, remarkably, also encode catalytic, self-splicing group I introns. After reconstituting and systematically investigating each of these biochemical activities for a candidate 'IStron' derived from Clostridium botulinum, we discovered sequence and structural features of the transposon-encoded RNA that satisfy molecular requirements of a group I intron and TnpB guide RNA, while still retaining the ability to be faithfully mobilized at the DNA level by the TnpA transposase. Strikingly, intron splicing was strongly repressed not only by TnpB, but also by the secondary structure of ωRNA alone, allowing the element to carefully control the relative levels of spliced products versus functional guide RNAs. Our results suggest that IStron transcripts have evolved a sensitive equilibrium to balance competing and mutually exclusive activities that promote transposon maintenance while limiting adverse fitness costs on the host. Collectively, this work explains how diverse enzymatic activities emerged during the selfish spread of IS607-family elements and highlights molecular innovation in the multi-functional utility of transposon-encoded noncoding RNAs.
Collapse
Affiliation(s)
- Rimantė Žedaveinytė
- Department of Biochemistry and Molecular Biophysics, Columbia University; New York, NY 10032, USA
| | - Chance Meers
- Department of Biochemistry and Molecular Biophysics, Columbia University; New York, NY 10032, USA
| | - Hoang C. Le
- Department of Biochemistry and Molecular Biophysics, Columbia University; New York, NY 10032, USA
| | - Edan E. Mortman
- Department of Genetics and Development, Columbia University; New York, NY 10032, USA
| | - Stephen Tang
- Department of Biochemistry and Molecular Biophysics, Columbia University; New York, NY 10032, USA
| | - George D. Lampe
- Department of Biochemistry and Molecular Biophysics, Columbia University; New York, NY 10032, USA
| | - Sanjana R. Pesari
- Department of Biochemistry and Molecular Biophysics, Columbia University; New York, NY 10032, USA
- Present address: Biochemistry and Molecular Biophysics Program, University of California, San Diego, CA, USA
| | - Diego R. Gelsinger
- Department of Biochemistry and Molecular Biophysics, Columbia University; New York, NY 10032, USA
| | - Tanner Wiegand
- Department of Biochemistry and Molecular Biophysics, Columbia University; New York, NY 10032, USA
| | - Samuel H. Sternberg
- Department of Biochemistry and Molecular Biophysics, Columbia University; New York, NY 10032, USA
| |
Collapse
|
7
|
Zhou K, Peng M, Deng N, Tan Z, Xiao N. Lactase bacteria in intestinal mucosa are associated with diarrhea caused by high-fat and high-protein diet. BMC Microbiol 2022; 22:226. [PMID: 36171559 PMCID: PMC9516839 DOI: 10.1186/s12866-022-02647-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 09/20/2022] [Indexed: 11/30/2022] Open
Abstract
Background Excessive fat and protein in food can cause diarrhea by disturbing the intestinal microecology. Lactase is a functional enzyme strongly associated with diarrhea, while lactase bacteria in the intestine are an important source of microbial lactase. Therefore, we reconnoiter the relationship between diarrhea induced by a high-fat and high-protein diet (HFHPD) and intestinal mucosal lactase bacteria from the perspective of functional genes. Result Operational Taxonomic Units (OTUs) were 23 and 31 in the normal group (NM) and model group (MD), respectively, and 11 of these were identical. The Chao1 and Observed specie indexes in the MD were higher than those in the NM, but this was not significant (P > 0.05). Meanwhile, the Principal coordinate analysis (PCoA) and Adonis test showed that the community structures of lactase bacteria in NM and MD were significantly different (P < 0.05). In taxonomic composition, lactase bacteria on the intestinal mucosa were sourced from Actinobacteria and Proteobacteria. Where Actinobacteria were higher in NM, and Proteobacteria were higher in MD. At the genus level, Bifidobacterium was the dominant genus (over 90% of the total). Compared to NM, the abundance of Bifidobacterium were lower in MD, while MD added sources for lactase bacteria of Rhizobium, Amycolatopsis, and Cedecea. Conclusions Our data demonstrate that HFHPD altered the community structure of lactase bacteria in the intestinal mucosa, decreased the abundance of the critical lactase bacteria, and promoted the occurrence of diarrhea.
Collapse
Affiliation(s)
- Kang Zhou
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Maijiao Peng
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Na Deng
- College of Chinese Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Zhoujin Tan
- Hunan Key Laboratory of TCM Prescription and Syndromes Translational Medicine, Changsha, Hunan, China.,College of Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Nenqun Xiao
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha, Hunan, China.
| |
Collapse
|