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Wan D, Cheng A, Wang Y, Zhong G, Li WV, Fan H. Analyzing RNA-Seq data from Chlamydia with super broad transcriptomic activation: challenges, solutions, and implications for other systems. BMC Genomics 2024; 25:801. [PMID: 39182031 PMCID: PMC11344909 DOI: 10.1186/s12864-024-10714-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Accepted: 08/16/2024] [Indexed: 08/27/2024] Open
Abstract
BACKGROUND RNA sequencing (RNA-Seq) offers profound insights into the complex transcriptomes of diverse biological systems. However, standard differential expression analysis pipelines based on DESeq2 and edgeR encounter challenges when applied to the immediate early transcriptomes of Chlamydia spp., obligate intracellular bacteria. These challenges arise from their reliance on assumptions that do not hold in scenarios characterized by extensive transcriptomic activation and limited repression. RESULTS Standard analyses using unique chlamydial RNA-Seq reads alone identify nearly 300 upregulated and about 300 downregulated genes, significantly deviating from actual RNA-Seq read trends. By incorporating both chlamydial and host reads or adjusting for total sequencing depth, the revised normalization methods each detected over 700 upregulated genes and 30 or fewer downregulated genes, closely aligned with observed RNA-Seq data. Further validation through qRT-PCR analysis confirmed the effectiveness of these adjusted approaches in capturing the true extent of transcriptomic activation during the immediate early phase of chlamydial infection. CONCLUSIONS This study highlights the limitations of standard RNA-Seq analysis tools in scenarios with extensive transcriptomic activation, such as in Chlamydia spp. during early infection. Our revised normalization methods, incorporating host reads or total sequencing depth, provide a more accurate representation of gene expression dynamics. These approaches may inform similar adjustments in other systems with unbalanced gene expression dynamics, enhancing the accuracy of transcriptomic analysis.
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Affiliation(s)
- Danny Wan
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Andrew Cheng
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Yuxuan Wang
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Guangming Zhong
- Department of Microbiology and Immunology, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Wei Vivian Li
- Department of Statistics, University of California Riverside, Riverside, CA, 92521, USA.
| | - Huizhou Fan
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA.
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Wan D, Cheng A, Wang Y, Zhong G, Li WV, Fan H. Analyzing RNA-Seq Data from Chlamydia with Super Broad Transcriptomic Activation: Challenges, Solutions, and Implications for Other Systems. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.16.594566. [PMID: 38826265 PMCID: PMC11142123 DOI: 10.1101/2024.05.16.594566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Motivation RNA sequencing (RNA-Seq) offers profound insights into the complex transcriptomes of diverse biological systems. However, standard differential expression analysis pipelines based on DESeq2 and edgeR encounter challenges when applied to the immediate early transcriptomes of Chlamydia spp., obligate intracellular bacteria. These challenges arise from their reliance on assumptions that do not hold in scenarios characterized by extensive transcriptomic activation and limited repression. Standard analyses using unique chlamydial RNA-Seq reads alone identify nearly 300 upregulated and about 300 downregulated genes, significantly deviating from actual RNA-Seq read trends. Results By incorporating both chlamydial and host reads or adjusting for total sequencing depth, the revised normalization methods each detected over 700 upregulated genes and 30 or fewer downregulated genes, closely aligned with observed RNA-Seq data. Further validation through qRT-PCR analysis confirmed the effectiveness of these adjusted approaches in capturing the true extent of transcriptomic activation during the immediate early phase of chlamydial infection. While the strategies employed are developed in the context of Chlamydia, the principles of flexible and context-aware normalization may inform adjustments in other systems with unbalanced gene expression dynamics, such as bacterial spore germination. Availability and implementation The code for reproducing the presented bioinformatic analysis is available at https://zenodo.org/records/11201379.
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Affiliation(s)
- Danny Wan
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - Andrew Cheng
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - Yuxuan Wang
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - Guangming Zhong
- Department of Microbiology and Immunology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Wei Vivian Li
- Department of Statistics, University of California Riverside, Riverside, CA92521, USA
| | - Huizhou Fan
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
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Wurihan W, Wang Y, Yeung S, Zou Y, Lai Z, Fondell JD, Li WV, Zhong G, Fan H. Expression activation of over 70% of Chlamydia trachomatis genes during the first hour of infection. Infect Immun 2024; 92:e0053923. [PMID: 38299827 PMCID: PMC10929459 DOI: 10.1128/iai.00539-23] [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: 01/02/2024] [Accepted: 01/09/2024] [Indexed: 02/02/2024] Open
Abstract
The obligate intracellular bacterium Chlamydia has a unique developmental cycle that alternates between two contrasting cell types. With a hardy envelope and highly condensed genome, the small elementary body (EB) maintains limited metabolic activities yet survives in extracellular environments and is infectious. After entering host cells, EBs differentiate into larger and proliferating reticulate bodies (RBs). Progeny EBs are derived from RBs in late developmental stages and eventually exit host cells. How expression of the chlamydial genome consisting of nearly 1,000 genes governs the chlamydial developmental cycle is unclear. A previous microarray study identified only 29 Chlamydia trachomatis immediate early genes, defined as genes with increased expression during the first hour postinoculation in cultured cells. In this study, we performed more sensitive RNA sequencing (RNA-Seq) analysis for C. trachomatis cultures with high multiplicities of infection. Remarkably, we observed well over 700 C. trachomatis genes that underwent 2- to 900-fold activation within 1 hour postinoculation. Quantitative reverse transcription real-time PCR analysis was further used to validate the activated expression of a large subset of the genes identified by RNA-Seq. Importantly, our results demonstrate that the immediate early transcriptome is over 20 times more extensive than previously realized. Gene ontology analysis indicates that the activated expression spans all functional categories. We conclude that over 70% of C. trachomatis genes are activated in EBs almost immediately upon entry into host cells, thus implicating their importance in initiating rapid differentiation into RBs and establishing an intracellular niche conducive with chlamydial development and growth.
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Affiliation(s)
- Wurihan Wurihan
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
| | - Yuxuan Wang
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Sydney Yeung
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Yi Zou
- Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Zhao Lai
- Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, Texas, USA
- Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Joseph D. Fondell
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Wei Vivian Li
- Department of Statistics, University of California Riverside, Riverside, California, USA
| | - Guangming Zhong
- Department of Microbiology and Immunology, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Huizhou Fan
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
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Lu B, Wang Y, Wurihan W, Cheng A, Yeung S, Fondell JD, Lai Z, Wan D, Wu X, Li WV, Fan H. Requirement of GrgA for Chlamydia infectious progeny production, optimal growth, and efficient plasmid maintenance. mBio 2024; 15:e0203623. [PMID: 38112466 PMCID: PMC10790707 DOI: 10.1128/mbio.02036-23] [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: 08/01/2023] [Accepted: 11/16/2023] [Indexed: 12/21/2023] Open
Abstract
IMPORTANCE Hallmarks of the developmental cycle of the obligate intracellular pathogenic bacterium Chlamydia are the primary differentiation of the infectious elementary body (EB) into the proliferative reticulate body (RB) and the secondary differentiation of RBs back into EBs. The mechanisms regulating these transitions remain unclear. In this report, we developed an effective novel strategy termed dependence on plasmid-mediated expression (DOPE) that allows for the knockdown of essential genes in Chlamydia. We demonstrate that GrgA, a Chlamydia-specific transcription factor, is essential for the secondary differentiation and optimal growth of RBs. We also show that GrgA, a chromosome-encoded regulatory protein, controls the maintenance of the chlamydial virulence plasmid. Transcriptomic analysis further indicates that GrgA functions as a critical regulator of all three sigma factors that recognize different promoter sets at developmental stages. The DOPE strategy outlined here should provide a valuable tool for future studies examining chlamydial growth, development, and pathogenicity.
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Affiliation(s)
- Bin Lu
- Department of Parasitology, Central South University Xiangya Medical School, Changsha, Hunan, China
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Yuxuan Wang
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Wurihan Wurihan
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Andrew Cheng
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Sydney Yeung
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Joseph D. Fondell
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Zhao Lai
- Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, Texas, USA
- Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Danny Wan
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Xiang Wu
- Department of Parasitology, Central South University Xiangya Medical School, Changsha, Hunan, China
| | - Wei Vivian Li
- Department of Statistics, University of California Riverside, Riverside, California, USA
| | - Huizhou Fan
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
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Hakiem OR, Rizvi SMA, Ramirez C, Tan M. Euo is a developmental regulator that represses late genes and activates midcycle genes in Chlamydia trachomatis. mBio 2023; 14:e0046523. [PMID: 37565751 PMCID: PMC10653925 DOI: 10.1128/mbio.00465-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/22/2023] [Indexed: 08/12/2023] Open
Abstract
IMPORTANCE In this study, we developed a correlative approach that combined DNA immunoprecipitation-seq and RNA-seq analyses to define the regulon of the Chlamydia trachomatis transcription factor Euo. We confirmed the proposed role of Euo as a transcriptional repressor of late chlamydial genes but also showed that Euo activates transcription of a subset of midcycle genes and autoregulates its own expression via negative feedback. This study validates and expands the role of Euo as an important developmental regulator in C. trachomatis. In addition, this genome-wide correlative approach can be applied to study transcription factors in other pathogenic bacteria.
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Affiliation(s)
- Owais R. Hakiem
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, California, USA
| | - Syed M. A. Rizvi
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, California, USA
| | - Cuper Ramirez
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, California, USA
| | - Ming Tan
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, California, USA
- Department of Medicine, University of California Irvine, Irvine, California, USA
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Jury B, Fleming C, Huston WM, Luu LDW. Molecular pathogenesis of Chlamydia trachomatis. Front Cell Infect Microbiol 2023; 13:1281823. [PMID: 37920447 PMCID: PMC10619736 DOI: 10.3389/fcimb.2023.1281823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/03/2023] [Indexed: 11/04/2023] Open
Abstract
Chlamydia trachomatis is a strict intracellular human pathogen. It is the main bacterial cause of sexually transmitted infections and the etiologic agent of trachoma, which is the leading cause of preventable blindness. Despite over 100 years since C. trachomatis was first identified, there is still no vaccine. However in recent years, the advancement of genetic manipulation approaches for C. trachomatis has increased our understanding of the molecular pathogenesis of C. trachomatis and progress towards a vaccine. In this mini-review, we aimed to outline the factors related to the developmental cycle phase and specific pathogenesis activity of C. trachomatis in order to focus priorities for future genetic approaches. We highlight the factors known to be critical for developmental cycle stages, gene expression regulatory factors, type III secretion system and their effectors, and individual virulence factors with known impacts.
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Affiliation(s)
- Brittany Jury
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia
| | - Charlotte Fleming
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia
| | | | - Laurence Don Wai Luu
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia
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Lu B, Wang Y, Wurihan W, Cheng A, Yeung S, Fondell JD, Lai Z, Wan D, Wu X, Li WV, Fan H. Requirement of GrgA for Chlamydia infectious progeny production, optimal growth, and efficient plasmid maintenance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.02.551707. [PMID: 37577610 PMCID: PMC10418237 DOI: 10.1101/2023.08.02.551707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Chlamydia, an obligate intracellular bacterial pathogen, has a unique developmental cycle involving the differentiation of invading elementary bodies (EBs) to noninfectious reticulate bodies (RBs), replication of RBs, and redifferentiation of RBs into progeny EBs. Progression of this cycle is regulated by three sigma factors, which direct the RNA polymerase to their respective target gene promoters. We hypothesized that the Chlamydia-specific transcriptional regulator GrgA, previously shown to activate σ66 and σ28, plays an essential role in chlamydial development and growth. To test this hypothesis, we applied a novel genetic tool known as dependence on plasmid-mediated expression (DOPE) to create Chlamydia trachomatis with conditional GrgA-deficiency. We show that GrgA-deficient C. trachomatis RBs have a growth rate that is approximately half of the normal rate and fail to transition into progeny EBs. In addition, GrgA-deficient C. trachomatis fail to maintain its virulence plasmid. Results of RNA-seq analysis indicate that GrgA promotes RB growth by optimizing tRNA synthesis and expression of nutrient-acquisition genes, while it enables RB-to-EB conversion by facilitating the expression of a histone and outer membrane proteins required for EB morphogenesis. GrgA also regulates numerous other late genes required for host cell exit and subsequent EB invasion into host cells. Importantly, GrgA stimulates the expression of σ54, the third and last sigma factor, and its activator AtoC, and thereby indirectly upregulating the expression of σ54-dependent genes. In conclusion, our work demonstrates that GrgA is a master transcriptional regulator in Chlamydia and plays multiple essential roles in chlamydial pathogenicity.
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Affiliation(s)
- Bin Lu
- Department of Parasitology, Central South University Xiangya Medical School, Changsha, Hunan 410013, China
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Yuxuan Wang
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Wurihan Wurihan
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Andrew Cheng
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Sydney Yeung
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Joseph D. Fondell
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Zhao Lai
- Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Danny Wan
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Xiang Wu
- Department of Parasitology, Central South University Xiangya Medical School, Changsha, Hunan 410013, China
| | - Wei Vivian Li
- Department of Statistics, University of California Riverside, Riverside, CA 92521, USA
| | - Huizhou Fan
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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Diversity of σ 66-Specific Promoters Contributes to Regulation of Developmental Gene Expression in Chlamydia trachomatis. J Bacteriol 2023; 205:e0031022. [PMID: 36598485 PMCID: PMC9879106 DOI: 10.1128/jb.00310-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Promoter recognition by the RNA polymerase (RNAP) holoenzyme is a key step in gene regulation. In Chlamydia trachomatis, a medically important obligate intracellular bacterium, σ66 allows the RNAP to initiate promoter-specific transcription throughout the chlamydial developmental cycle. Here, we investigated the intrinsic properties of σ66-specific promoters with emphasis on their role in the developmental gene expression of C. trachomatis. First, we examined whether promoters that contain a 5'-T(-15)G(-14)-3' (TG) motif upstream from the -10 element appear more often than others in genes that are preferentially expressed during the early, middle, or late stages of the C. trachomatis developmental cycle. We then determined the critical genetic elements that are required for transcription initiation in vitro. We also assessed the activity of promoters in the presence of Scc4, which can directly interact with σ66RNAP. Finally, we evaluated the promoter-specific dynamics during C. trachomatis infection using a reporter assay. These results reveal that the TG motif is an important determinant in certain early or late promoters. The TG promoters that have the -35 element are recognized by σ66RNAP and Scc4 differently from those lacking the -35 element. Based on these properties, the σ66-specific promoters can fall into three classes. Architectural diversity, behavioral plasticity, and the specific interplays between promoters and the σ66RNAP likely contribute to developmental gene transcription in C. trachomatis. IMPORTANCE Meticulous promoter elucidation is required to understand the foundations of transcription initiation. However, knowledge of promoter-specific transcription remains limited in C. trachomatis. This work underscores the structural and functional plasticity of σ66-specific promoters that are regulated by σ66RNAP, as well as their importance in the developmental gene regulation of C. trachomatis.
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Better In Vitro Tools for Exploring Chlamydia trachomatis Pathogenesis. LIFE (BASEL, SWITZERLAND) 2022; 12:life12071065. [PMID: 35888153 PMCID: PMC9323215 DOI: 10.3390/life12071065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/05/2022] [Accepted: 07/14/2022] [Indexed: 11/21/2022]
Abstract
Currently, Chlamydia trachomatis still possesses a significant impact on public health, with more than 130 million new cases each year, alongside a high prevalence of asymptomatic infections (approximately 80% in women and 50% in men). C. trachomatis infection involves a wide range of different cell types, from cervical epithelial cells, testicular Sertoli cells to Synovial cells, leading to a broad spectrum of pathologies of varying severity both in women and in men. Several two-dimensional in vitro cellular models have been employed for investigating C. trachomatis host–cell interaction, although they present several limitations, such as the inability to mimic the complex and dynamically changing structure of in vivo human host-tissues. Here, we present a brief overview of the most cutting-edge three-dimensional cell-culture models that mimic the pathophysiology of in vivo human tissues and organs for better translating experimental findings into a clinical setting. Future perspectives in the field of C. trachomatis research are also provided.
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Huang Y, Wurihan W, Lu B, Zou Y, Wang Y, Weldon K, Fondell JD, Lai Z, Wu X, Fan H. Robust Heat Shock Response in Chlamydia Lacking a Typical Heat Shock Sigma Factor. Front Microbiol 2022; 12:812448. [PMID: 35046926 PMCID: PMC8762339 DOI: 10.3389/fmicb.2021.812448] [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: 11/10/2021] [Accepted: 12/02/2021] [Indexed: 11/13/2022] Open
Abstract
Cells reprogram their transcriptome in response to stress, such as heat shock. In free-living bacteria, the transcriptomic reprogramming is mediated by increased DNA-binding activity of heat shock sigma factors and activation of genes normally repressed by heat-induced transcription factors. In this study, we performed transcriptomic analyses to investigate heat shock response in the obligate intracellular bacterium Chlamydia trachomatis, whose genome encodes only three sigma factors and a single heat-induced transcription factor. Nearly one-third of C. trachomatis genes showed statistically significant (≥1.5-fold) expression changes 30 min after shifting from 37 to 45°C. Notably, chromosomal genes encoding chaperones, energy metabolism enzymes, type III secretion proteins, as well as most plasmid-encoded genes, were differentially upregulated. In contrast, genes with functions in protein synthesis were disproportionately downregulated. These findings suggest that facilitating protein folding, increasing energy production, manipulating host activities, upregulating plasmid-encoded gene expression, and decreasing general protein synthesis helps facilitate C. trachomatis survival under stress. In addition to relieving negative regulation by the heat-inducible transcriptional repressor HrcA, heat shock upregulated the chlamydial primary sigma factor σ66 and an alternative sigma factor σ28. Interestingly, we show for the first time that heat shock downregulates the other alternative sigma factor σ54 in a bacterium. Downregulation of σ54 was accompanied by increased expression of the σ54 RNA polymerase activator AtoC, thus suggesting a unique regulatory mechanism for reestablishing normal expression of select σ54 target genes. Taken together, our findings reveal that C. trachomatis utilizes multiple novel survival strategies to cope with environmental stress and even to replicate. Future strategies that can specifically target and disrupt Chlamydia’s heat shock response will likely be of therapeutic value.
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Affiliation(s)
- Yehong Huang
- Department of Parasitology, Xiangya School of Basic Medicine, Central South University, Changsha, China.,Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, United States
| | - Wurihan Wurihan
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, United States
| | - Bin Lu
- Department of Parasitology, Xiangya School of Basic Medicine, Central South University, Changsha, China.,Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, United States
| | - Yi Zou
- Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX, United States
| | - Yuxuan Wang
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, United States
| | - Korri Weldon
- Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX, United States
| | - Joseph D Fondell
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, United States
| | - Zhao Lai
- Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX, United States.,Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, TX, United States
| | - Xiang Wu
- Department of Parasitology, Xiangya School of Basic Medicine, Central South University, Changsha, China
| | - Huizhou Fan
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, United States
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