Functional Similarity of PRD-Containing Virulence Regulators in Bacillus Anthracis
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The Texas Medical Center Library DigitalCommons@TMC The University of Texas MD Anderson Cancer Center UTHealth Graduate School of The University of Texas MD Anderson Cancer Biomedical Sciences Dissertations and Theses Center UTHealth Graduate School of (Open Access) Biomedical Sciences 5-2018 Functional Similarity of PRD-Containing Virulence Regulators in Bacillus anthracis Malik Raynor Follow this and additional works at: https://digitalcommons.library.tmc.edu/utgsbs_dissertations Part of the Bacteriology Commons, Biochemistry Commons, Molecular Biology Commons, Molecular Genetics Commons, and the Pathogenic Microbiology Commons Recommended Citation Raynor, Malik, "Functional Similarity of PRD-Containing Virulence Regulators in Bacillus anthracis" (2018). The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Dissertations and Theses (Open Access). 857. https://digitalcommons.library.tmc.edu/utgsbs_dissertations/857 This Dissertation (PhD) is brought to you for free and open access by the The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences at DigitalCommons@TMC. It has been accepted for inclusion in The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Dissertations and Theses (Open Access) by an authorized administrator of DigitalCommons@TMC. For more information, please contact [email protected]. FUNCTIONAL SIMILARITY OF PRD-CONTAINING VIRULENCE REGULATORS IN BACILLUS ANTHRACIS by Malik Jamaal Raynor, B.S. APPROVED: ______________________________ Theresa M. Koehler, Ph.D. Advisory Professor ______________________________ Peter J. Christie, Ph.D. ______________________________ Kevin A. Morano, Ph.D. ______________________________ Hung Ton-That, Ph.D. ______________________________ Eric J. Wagner, Ph.D. APPROVED: ____________________________ Dean, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences FUNCTIONAL SIMILARITY OF PRD-CONTAINING VIRULENCE REGULATORS IN BACILLUS ANTHRACIS A DISSERTATION Presented to the Faculty of The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences in Partial Fulfillment of the Requirements for the Degree of DOCTOR OF PHILOSOPHY by Malik Jamaal Raynor, B.S. Houston, Texas Date of Graduation (May, 2018) FUNCTIONAL SIMILARITY OF PRD-CONTAINING VIRULENCE REGULATORS IN BACILLUS ANTHRACIS Malik Jamaal Raynor, B.S. Advisory Professor: Theresa M. Koehler, Ph.D. Bacillus anthracis produces three regulators, AtxA, AcpA, and AcpB, that control virulence gene expression and are members of an emerging class of regulators termed “PCVRs” (Phosphoenolpyruvate-dependent phosphotransferase regulation Domain-Containing Virulence Regulators). AtxA controls expression of the toxin genes; lef, cya, and pag, and is the master virulence regulator and archetype PCVR. AcpA and AcpB are less well studied. AcpA and AcpB independently positively control transcription of the capsule biosynthetic operon capBCADE, and culture conditions that enhance AtxA activity result in capBCADE transcription in strains lacking acpA and acpB. RNA-Seq was used to assess the regulons of the paralogs in strains producing individual PCVRs at native levels. Plasmid- and chromosome-borne genes were PCVR-controlled, with AtxA, AcpA, and AcpB having a ≥4-fold effect on transcript levels of 145, 130, and 49 genes respectively. Several genes were co-regulated by two or three PCVRs. Results from transcriptional reporters of PCVR-regulated promoters fused to promoterless lacZ genes largely mirrored RNA-Seq data showing AtxA alone had activity on Plef-lacZ, and AcpA and AcpB had more activity than AtxA on PcapB-lacZ. Studies to test the effect of AtxA levels on virulence and sporulation used atxA mutants. A mutant that overexpressed atxA and exhibited elevated AtxA and toxin levels in vitro, was not increased for virulence in a murine anthrax infection model. AtxA levels also affected sporulation efficiency. Culture of B. anthracis in medium containing bicarbonate and elevated carbon dioxide increased PCVR activity compared to culture in ambient air in medium lacking bicarbonate. However, neither the solubility nor stability of the regulators was affected by carbon dioxide concentration. AcpA and AcpB form homomultimers and multimerization was dependent on the iii EIIB-like domains, as shown previously for AtxA. Heteromultimers of AtxA-AcpA were detected and in co-expression experiments, AcpA activity was reduced by increased levels of AtxA. An AtxA orthologue in Bacillus cereus, AtxA2, had less activity than AtxA from B. anthracis potentially due to reduced dimer formation. The results provided in this dissertation increase our knowledge of virulence gene expression in B. anthracis, while advancing our understanding of this newly-discovered class of transcriptional regulators. iv Table of Contents Approval Sheet..............................................................................................................................i Title Page......................................................................................................................................ii Abstract........................................................................................................................................iii Table of Contents.........................................................................................................................v List of Figures.............................................................................................................................viii List of Tables................................................................................................................................x Chapter I: Introduction...............................................................................................................1 1.1 Gene expression modulated by environmental conditions.........................................2 1.2 PRD-containing virulence regulators..........................................................................5 1.3 Bacillus anthracis and anthrax disease......................................................................7 1.4 Virulence factors in anthrax pathogenesis.................................................................9 1.5 AtxA: the most well-characterized PCVR.................................................................11 1.6 AcpA and AcpB: regulators of capsule expression...................................................14 1.7 AtxA2, an AtxA homologue in Bacillus cereus strain G9241....................................14 1.8 Gaps in knowledge and significance of this work.....................................................15 Chapter II: Materials and Methods..........................................................................................17 2.1 Culture conditions.....................................................................................................18 2.2 Strain construction....................................................................................................18 2.3 Native and IPTG-induced PCVR expression............................................................21 2.4 RNA isolation for RNA-seq.......................................................................................21 2.5 Creation of Next Generation Sequencing (NGS) libraries for RNA-seq and sequencing..................................................................................................22 2.6 RNA-seq and bioinformatic analysis.........................................................................23 2.7 Western blotting........................................................................................................24 2.8 India ink exclusion assay..........................................................................................25 v 2.9 Co-affinity purification...............................................................................................25 2.10 AcpA-His and AcpB-His purification.......................................................................26 2.11 Bis-maleimidohexane crosslinking.........................................................................26 2.12 Mouse infections.....................................................................................................27 2.13 Heat-resistant CFU determination..........................................................................27 2.14 Real-time quantitative PCR (RT-qPCR).................................................................28 Chapter III: Regulons of PRD-containing Bacillus anthracis virulence regulators reveal overlapping but distinct functions..........................................................35 3.1 Introduction...............................................................................................................36 3.2 Results......................................................................................................................38 3.2.1 Amino acid sequence and predicted domain similarity of the B. anthracis PCVRs...................................................................................38 3.2.2 Native PCVR protein and transcript levels.................................................41 3.2.3 Overlapping regulons of AtxA, AcpA, and AcpB........................................45 3.2.4 Loci of PCVR-regulated genes..................................................................49