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Ryan D, Bornet E, Prezza G, Alampalli SV, Franco de Carvalho T, Felchle H, Ebbecke T, Hayward RJ, Deutschbauer AM, Barquist L, Westermann AJ. An expanded transcriptome atlas for Bacteroides thetaiotaomicron reveals a small RNA that modulates tetracycline sensitivity. Nat Microbiol 2024; 9:1130-1144. [PMID: 38528147 PMCID: PMC10994844 DOI: 10.1038/s41564-024-01642-9] [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: 02/17/2023] [Accepted: 02/07/2024] [Indexed: 03/27/2024]
Abstract
Plasticity in gene expression allows bacteria to adapt to diverse environments. This is particularly relevant in the dynamic niche of the human intestinal tract; however, transcriptional networks remain largely unknown for gut-resident bacteria. Here we apply differential RNA sequencing (RNA-seq) and conventional RNA-seq to the model gut bacterium Bacteroides thetaiotaomicron to map transcriptional units and profile their expression levels across 15 in vivo-relevant growth conditions. We infer stress- and carbon source-specific transcriptional regulons and expand the annotation of small RNAs (sRNAs). Integrating this expression atlas with published transposon mutant fitness data, we predict conditionally important sRNAs. These include MasB, which downregulates tetracycline tolerance. Using MS2 affinity purification and RNA-seq, we identify a putative MasB target and assess its role in the context of the MasB-associated phenotype. These data-publicly available through the Theta-Base web browser ( http://micromix.helmholtz-hiri.de/bacteroides/ )-constitute a valuable resource for the microbiome community.
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Affiliation(s)
- Daniel Ryan
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Elise Bornet
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Gianluca Prezza
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Shuba Varshini Alampalli
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Taís Franco de Carvalho
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Hannah Felchle
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
- Department of Radiation Oncology, Technical University of Munich, School of Medicine, Klinikum rechts der Isar, Munich, Germany
| | - Titus Ebbecke
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Regan J Hayward
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Adam M Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
- Faculty of Medicine, University of Würzburg, Würzburg, Germany
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Alexander J Westermann
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany.
- Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany.
- Department of Microbiology, Biocentre, University of Würzburg, Würzburg, Germany.
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Ryan D, Bornet E, Prezza G, Alampalli SV, de Carvalho TF, Felchle H, Ebbecke T, Hayward R, Deutschbauer AM, Barquist L, Westermann AJ. An integrated transcriptomics-functional genomics approach reveals a small RNA that modulates Bacteroides thetaiotaomicron sensitivity to tetracyclines. bioRxiv 2023:2023.02.16.528795. [PMID: 36824877 PMCID: PMC9949090 DOI: 10.1101/2023.02.16.528795] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Gene expression plasticity allows bacteria to adapt to diverse environments, tie their metabolism to available nutrients, and cope with stress. This is particularly relevant in a niche as dynamic and hostile as the human intestinal tract, yet transcriptional networks remain largely unknown in gut Bacteroides spp. Here, we map transcriptional units and profile their expression levels in Bacteroides thetaiotaomicron over a suite of 15 defined experimental conditions that are relevant in vivo , such as variation of temperature, pH, and oxygen tension, exposure to antibiotic stress, and growth on simple carbohydrates or on host mucin-derived glycans. Thereby, we infer stress- and carbon source-specific transcriptional regulons, including conditional expression of capsular polysaccharides and polysaccharide utilization loci, and expand the annotation of small regulatory RNAs (sRNAs) in this organism. Integrating this comprehensive expression atlas with transposon mutant fitness data, we identify conditionally important sRNAs. One example is MasB, whose inactivation led to increased bacterial tolerance of tetracyclines. Using MS2 affinity purification coupled with RNA sequencing, we predict targets of this sRNA and discuss their potential role in the context of the MasB-associated phenotype. Together, this transcriptomic compendium in combination with functional sRNA genomics-publicly available through a new iteration of the 'Theta-Base' web browser (www.helmholtz-hiri.de/en/datasets/bacteroides-v2)-constitutes a valuable resource for the microbiome and sRNA research communities alike.
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Rakshit S, Hingankar N, Alampalli SV, Adiga V, Sundararaj BK, Sahoo PN, Finak G, Uday Kumar J AJ, Dhar C, D'Souza G, Virkar RG, Ghate M, Thakar MR, Paranjape RS, De Rosa SC, Ottenhoff THM, Vyakarnam A. HIV Skews a Balanced Mtb-Specific Th17 Response in Latent Tuberculosis Subjects to a Pro-inflammatory Profile Independent of Viral Load. Cell Rep 2020; 33:108451. [PMID: 33264614 DOI: 10.1016/j.celrep.2020.108451] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 09/15/2020] [Accepted: 11/09/2020] [Indexed: 02/08/2023] Open
Abstract
HIV infection predisposes latent tuberculosis-infected (LTBI) subjects to active TB. This study is designed to determine whether HIV infection of LTBI subjects compromises the balanced Mycobacterium tuberculosis (Mtb)-specific T helper 17 (Th17) response of recognized importance in anti-TB immunity. Comparative analysis of Mtb- and cytomegalovirus (CMV)-specific CD4+ T cell responses demonstrates a marked dampening of the Mtb-specific CD4+ T cell effectors and polyfunctional cells while preserving CMV-specific response. Additionally, HIV skews the Mtb-specific Th17 response in chronic HIV-infected LTBI progressors, but not long-term non-progressors (LTNPs), with preservation of pro-inflammatory interferon (IFN)-γ+/interleukin-17+ (IL-17+) and significant loss of anti-inflammatory IL-10+/IL-17+ effectors that is restored by anti-retroviral therapy (ART). HIV-driven impairment of Mtb-specific response cannot be attributed to preferential infection as cell-associated HIV DNA and HIV RNA reveal equivalent viral burden in CD4+ T cells from different antigen specificities. We therefore propose that beyond HIV-induced loss of Mtb-specific CD4+ T cells, the associated dysregulation of Mtb-specific T cell homeostasis can potentially enhance the onset of TB in LTBI subjects.
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Affiliation(s)
- Srabanti Rakshit
- Laboratory of Immunology of HIV-TB Co-infection, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, India
| | - Nitin Hingankar
- Laboratory of Immunology of HIV-TB Co-infection, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, India
| | - Shuba Varshini Alampalli
- Laboratory of Immunology of HIV-TB Co-infection, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, India
| | - Vasista Adiga
- Laboratory of Immunology of HIV-TB Co-infection, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, India
| | - Bharath K Sundararaj
- Laboratory of Immunology of HIV-TB Co-infection, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, India
| | - Pravat Nalini Sahoo
- Laboratory of Immunology of HIV-TB Co-infection, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, India
| | - Greg Finak
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Anto Jesuraj Uday Kumar J
- Departments of Infectious Diseases & Pulmonary Medicine, St. John's Research Institute, Bangalore, India
| | - Chirag Dhar
- Departments of Infectious Diseases & Pulmonary Medicine, St. John's Research Institute, Bangalore, India
| | - George D'Souza
- Departments of Infectious Diseases & Pulmonary Medicine, St. John's Research Institute, Bangalore, India
| | | | - Manisha Ghate
- National Aids Research Institute, Bhosari, Pune, Maharashtra, India
| | - Madhuri R Thakar
- National Aids Research Institute, Bhosari, Pune, Maharashtra, India
| | | | - Stephen C De Rosa
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Tom H M Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - Annapurna Vyakarnam
- Laboratory of Immunology of HIV-TB Co-infection, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, India; Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, Faculty of Life Sciences & Medicine, Guy's Hospital, King's College London, London SE1 9RT, UK.
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Alampalli SV, Thomson MM, Sampathkumar R, Sivaraman K, U. K. J. AJ, Dhar C, D. Souza G, Berry N, Vyakarnam A. Deep sequencing of near full-length HIV-1 genomes from plasma identifies circulating subtype C and infrequent occurrence of AC recombinant form in Southern India. PLoS One 2017; 12:e0188603. [PMID: 29220350 PMCID: PMC5722309 DOI: 10.1371/journal.pone.0188603] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [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: 09/08/2017] [Accepted: 11/09/2017] [Indexed: 01/25/2023] Open
Abstract
India has the third largest number of HIV-1-infected individuals accounting for approximately 2.1 million people, with a predominance of circulating subtype C strains and a low prevalence of subtype A and A1C and BC recombinant forms, identified over the past two decades. Recovery of near full-length HIV-1 genomes from a plasma source coupled with advances in next generation sequencing (NGS) technologies and development of universal methods for amplifying whole genomes of HIV-1 circulating in a target geography or population provides the opportunity for a detailed analysis of HIV-1 strain identification, evolution and dynamics. Here we describe the development and implementation of approaches for HIV-1 NGS analysis in a southern Indian cohort. Plasma samples (n = 20) were obtained from HIV-1-confirmed individuals living in and around the city of Bengaluru. Near full-length genome recovery was obtained for 9 Indian HIV-1 patients, with recovery of full-length gag and env genes for 10 and 2 additional subjects, respectively. Phylogenetic analyses indicate the majority of sequences to be represented by subtype C viruses branching within a monophyletic clade, comprising viruses from India, Nepal, Myanmar and China and closely related to a southern African cluster, with a low prevalence of the A1C recombinant form also present. Development of algorithms for bespoke recovery and analysis at a local level will further aid clinical management of HIV-1 infected Indian subjects and delineate the progress of the HIV-1 pandemic in this and other geographical regions.
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Affiliation(s)
| | - Michael M. Thomson
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Majadahonda, Madrid, Spain
| | - Raghavan Sampathkumar
- Centre for Infectious Disease Research (CIDR), Indian Institute of Science, Bengaluru, India
| | - Karthi Sivaraman
- Centre for Infectious Disease Research (CIDR), Indian Institute of Science, Bengaluru, India
| | | | - Chirag Dhar
- Department of Infectious Diseases, St John’s Research Institute, Bengaluru, India
| | - George D. Souza
- Department of Pulmonary Medicine & Department of Infectious Diseases, St John’s Research Institute, Bengaluru, India
| | - Neil Berry
- Division of Virology, NIBSC, South Mimms, United Kingdom
| | - Annapurna Vyakarnam
- Centre for Infectious Disease Research (CIDR), Indian Institute of Science, Bengaluru, India
- Department of Infectious Diseases, King’s College London, London, United Kingdom
- * E-mail: ,
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Alampalli SV, Grover M, Chandran S, Tatu U, Acharya P. Proteome and Structural Organization of the Knob Complex on the Surface of the Plasmodium
Infected Red Blood Cell. Proteomics Clin Appl 2017; 12:e1600177. [DOI: 10.1002/prca.201600177] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 08/16/2017] [Indexed: 02/04/2023]
Affiliation(s)
| | - Manish Grover
- Department of Biochemistry; Indian Institute of Science; Bangalore India
| | - Syama Chandran
- Department of Biochemistry; Indian Institute of Science; Bangalore India
| | - Utpal Tatu
- Department of Biochemistry; Indian Institute of Science; Bangalore India
| | - Pragyan Acharya
- Department of Biochemistry; All India Institute of Medical Sciences; New Delhi India
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Chatterjee S, Alampalli SV, Nageshan RK, Chettiar ST, Joshi S, Tatu US. Draft genome of a commonly misdiagnosed multidrug resistant pathogen Candida auris. BMC Genomics 2015; 16:686. [PMID: 26346253 PMCID: PMC4562351 DOI: 10.1186/s12864-015-1863-z] [Citation(s) in RCA: 164] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 08/18/2015] [Indexed: 12/16/2022] Open
Abstract
Background Candida auris is a multidrug resistant, emerging agent of fungemia in humans. Its actual global distribution remains obscure as the current commercial methods of clinical diagnosis misidentify it as C. haemulonii. Here we report the first draft genome of C. auris to explore the genomic basis of virulence and unique differences that could be employed for differential diagnosis. Results More than 99.5 % of the C. auris genomic reads did not align to the current whole (or draft) genome sequences of Candida albicans, Candida lusitaniae, Candida glabrata and Saccharomyces cerevisiae; thereby indicating its divergence from the active Candida clade. The genome spans around 12.49 Mb with 8527 predicted genes. Functional annotation revealed that among the sequenced Candida species, it is closest to the hemiascomycete species Clavispora lusitaniae. Comparison with the well-studied species Candida albicans showed that it shares significant virulence attributes with other pathogenic Candida species such as oligopeptide transporters, mannosyl transfersases, secreted proteases and genes involved in biofilm formation. We also identified a plethora of transporters belonging to the ABC and major facilitator superfamily along with known MDR transcription factors which explained its high tolerance to antifungal drugs. Conclusions Our study emphasizes an urgent need for accurate fungal screening methods such as PCR and electrophoretic karyotyping to ensure proper management of fungemia. Our work highlights the potential genetic mechanisms involved in virulence and pathogenicity of an important emerging human pathogen namely C. auris. Owing to its diversity at the genomic scale; we expect the genome sequence to be a useful resource to map species specific differences that will help develop accurate diagnostic markers and better drug targets. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1863-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sharanya Chatterjee
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India, 560012.
| | | | - Rishi Kumar Nageshan
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India, 560012.
| | - Sivarajan T Chettiar
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India, 560012.
| | | | - Utpal S Tatu
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India, 560012.
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Chatterjee S, Alampalli SV, Nageshan RK, Chettiar ST, Joshi S, Tatu US. Draft genome of a commonly misdiagnosed multidrug resistant pathogen Candida auris. BMC Genomics 2015. [PMID: 26346253 DOI: 10.1186/s12864-015-1863-z.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Candida auris is a multidrug resistant, emerging agent of fungemia in humans. Its actual global distribution remains obscure as the current commercial methods of clinical diagnosis misidentify it as C. haemulonii. Here we report the first draft genome of C. auris to explore the genomic basis of virulence and unique differences that could be employed for differential diagnosis. RESULTS More than 99.5 % of the C. auris genomic reads did not align to the current whole (or draft) genome sequences of Candida albicans, Candida lusitaniae, Candida glabrata and Saccharomyces cerevisiae; thereby indicating its divergence from the active Candida clade. The genome spans around 12.49 Mb with 8527 predicted genes. Functional annotation revealed that among the sequenced Candida species, it is closest to the hemiascomycete species Clavispora lusitaniae. Comparison with the well-studied species Candida albicans showed that it shares significant virulence attributes with other pathogenic Candida species such as oligopeptide transporters, mannosyl transfersases, secreted proteases and genes involved in biofilm formation. We also identified a plethora of transporters belonging to the ABC and major facilitator superfamily along with known MDR transcription factors which explained its high tolerance to antifungal drugs. CONCLUSIONS Our study emphasizes an urgent need for accurate fungal screening methods such as PCR and electrophoretic karyotyping to ensure proper management of fungemia. Our work highlights the potential genetic mechanisms involved in virulence and pathogenicity of an important emerging human pathogen namely C. auris. Owing to its diversity at the genomic scale; we expect the genome sequence to be a useful resource to map species specific differences that will help develop accurate diagnostic markers and better drug targets.
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Affiliation(s)
- Sharanya Chatterjee
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India, 560012.
| | | | - Rishi Kumar Nageshan
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India, 560012.
| | - Sivarajan T Chettiar
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India, 560012.
| | | | - Utpal S Tatu
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India, 560012.
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