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Shore SFH, Ptacek M, Steen AD, Fozo EM. A simple BLASTn-based approach generates novel insights into the regulation and biological function of type I toxin-antitoxins. mSystems 2024:e0120423. [PMID: 38856235 DOI: 10.1128/msystems.01204-23] [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: 11/14/2023] [Accepted: 05/01/2024] [Indexed: 06/11/2024] Open
Abstract
Bacterial chromosomal type I toxin-antitoxin systems consist of a small protein, typically under 60 amino acids, and a small RNA (sRNA) that represses toxin translation. These gene pairs have gained attention over the last decade for their contribution to antibiotic persistence and phage tolerance in bacteria. However, biological functions for many remain elusive as gene deletions often fail to produce an observable phenotype. For many pairs, it is still unknown when the toxin and/or antitoxin gene are natively expressed within the bacterium. We examined sequence conservation of three type I toxin-antitoxin systems, tisB/istR-1, shoB/ohsC, and zor/orz, in over 2,000 Escherichia coli strains, including pathogenic and commensal isolates. Using our custom database, we found that these gene pairs are widespread across E. coli and have expression potential via BLASTn. We identified an alternative, dominant sequence variant of TisB and confirmed that it is toxic upon overproduction. Additionally, analyses revealed a highly conserved sequence in the zorO mRNA untranslated region that is required for full toxicity. We further noted that over 30% of E. coli genomes contain an orz antitoxin gene only and confirmed its expression in a representative strain: the first confirmed report of a type I antitoxin without its cognate toxin. Our results add to our understanding of these systems, and our methodology is applicable for other type I loci to identify critical regulatory and functional features.IMPORTANCEChromosomal type I toxin-antitoxins are a class of genes that have gained increasing attention over the last decade for their roles in antibiotic persistence which may contribute to therapeutic failures. However, the control of many of these genes and when they function have remained elusive. We demonstrate that a simple genetic conservation-based approach utilizing free, publicly available data yields known and novel insights into the regulation and function of three chromosomal type I toxin-antitoxins in Escherichia coli. This study also provides a framework for how this approach could be applied to other genes of interest.
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Affiliation(s)
- Selene F H Shore
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Michael Ptacek
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Andrew D Steen
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
- Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, Tennessee, USA
| | - Elizabeth M Fozo
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
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Yang S, Sheffer M, Kaplan IE, Wang Z, Tarannum M, Dinh K, Abdulhamid Y, Shapiro R, Porter R, Soiffer R, Ritz J, Koreth J, Wei Y, Chen P, Zhang K, Márquez-Pellegrin V, Bonanno S, Joshi N, Guan M, Yang M, Li D, Bellini C, Chen J, Wu CJ, Barbie D, Li J, Romee R. Nonpathogenic E. coli engineered to surface display cytokines as a new platform for immunotherapy. RESEARCH SQUARE 2024:rs.3.rs-4031911. [PMID: 38562821 PMCID: PMC10984091 DOI: 10.21203/rs.3.rs-4031911/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Given the safety, tumor tropism, and ease of genetic manipulation in non-pathogenic Escherichia coli (E. coli), we designed a novel approach to deliver biologics to overcome poor trafficking and exhaustion of immune cells in the tumor microenvironment, via the surface display of key immune-activating cytokines on the outer membrane of E. coli K-12 DH5α. Bacteria expressing murine decoy-resistant IL18 mutein (DR18) induced robust CD8+ T and NK cell-dependent immune responses leading to dramatic tumor control, extending survival, and curing a significant proportion of immune-competent mice with colorectal carcinoma and melanoma. The engineered bacteria demonstrated tumor tropism, while the abscopal and recall responses suggested epitope spreading and induction of immunologic memory. E. coli K-12 DH5α engineered to display human DR18 potently activated mesothelin-targeting CAR NK cells and safely enhanced their trafficking into the tumors, leading to improved control and survival in xenograft mice bearing mesothelioma tumor cells, otherwise resistant to NK cells. Gene expression analysis of the bacteria-primed CAR NK cells showed enhanced TNFα signaling via NFkB and upregulation of multiple activation markers. Our novel live bacteria-based immunotherapeutic platform safely and effectively induces potent anti-tumor responses in otherwise hard-to-treat solid tumors, motivating further evaluation of this approach in the clinic.
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Affiliation(s)
- Shaobo Yang
- Department of Bioengineering, Northeastern University, Boston, MA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Michal Sheffer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Isabel E Kaplan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Zongqi Wang
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI
| | - Mubin Tarannum
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Khanhlinh Dinh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Yasmin Abdulhamid
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Roman Shapiro
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Rebecca Porter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Robert Soiffer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Jerome Ritz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - John Koreth
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Yun Wei
- Department of Chemistry and Chemical Engineering, Northeastern University, Boston, MA
| | - Peiru Chen
- Department of Chemistry and Chemical Engineering, Northeastern University, Boston, MA
| | - Ke Zhang
- Department of Bioengineering, Northeastern University, Boston, MA
- Department of Chemistry and Chemical Engineering, Northeastern University, Boston, MA
| | | | - Shanna Bonanno
- Department of Bioengineering, Northeastern University, Boston, MA
| | - Neel Joshi
- Department of Chemistry and Chemical Engineering, Northeastern University, Boston, MA
| | - Ming Guan
- Department of Bioengineering, Northeastern University, Boston, MA
| | - Mengdi Yang
- Department of Bioengineering, Northeastern University, Boston, MA
| | - Deng Li
- Department of Bioengineering, Northeastern University, Boston, MA
| | - Chiara Bellini
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Jianzhu Chen
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA
| | - Catherine J. Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - David Barbie
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Jiahe Li
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI
| | - Rizwan Romee
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
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Sit B, Lamason RL. Pathogenic Rickettsia spp. as emerging models for bacterial biology. J Bacteriol 2024; 206:e0040423. [PMID: 38315013 PMCID: PMC10883807 DOI: 10.1128/jb.00404-23] [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] [Indexed: 02/07/2024] Open
Abstract
Our understanding of free-living bacterial models like Escherichia coli far outpaces that of obligate intracellular bacteria, which cannot be cultured axenically. All obligate intracellular bacteria are host-associated, and many cause serious human diseases. Their constant exposure to the distinct biochemical niche of the host has driven the evolution of numerous specialized bacteriological and genetic adaptations, as well as innovative molecular mechanisms of infection. Here, we review the history and use of pathogenic Rickettsia species, which cause an array of vector-borne vascular illnesses, as model systems to probe microbial biology. Although many challenges remain in our studies of these organisms, the rich pathogenic and biological diversity of Rickettsia spp. constitutes a unique backdrop to investigate how microbes survive and thrive in host and vector cells. We take a bacterial-focused perspective and highlight emerging insights that relate to new host-pathogen interactions, bacterial physiology, and evolution. The transformation of Rickettsia spp. from pathogens to models demonstrates how recalcitrant microbes may be leveraged in the lab to tap unmined bacterial diversity for new discoveries. Rickettsia spp. hold great promise as model systems not only to understand other obligate intracellular pathogens but also to discover new biology across and beyond bacteria.
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Affiliation(s)
- Brandon Sit
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Rebecca L. Lamason
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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