ClpC operon regulates cell architecture and sporulation in Bacillus anthracis Lalit K. Singh*, Neha Dhasmana*, Andaleeb Sajid, Prasun Kumar, Asani Bhaduri, Mitasha Bharadwaj, Sheetal Gandotra, Vipin C. Kalia, Taposh K Das¶, Ajay K. Goel§, Andrei P. Pomerantsev†, Richa Misra , Ulf Gerth±, Stephen H. Leppla† and Yogendra Singh Figure S1 A. Figure S1 A. ClpC operon organization in B. anthracis. ClpC operon comprising of four genes: ctsR, mcsA, mcsB and clpC. Deletions were made by homologous recombination using intragenic regions of respective genes. All deletions were inframe maintaining normal expression of downstream genes in the operon. Figure S1 B Figure S1 B. Confirmation of mutants by polymerase chain reaction. Genomic DNA was isolated from Bacillus anthracis Sterne and mutant strains. The gene encoding for CtsR, McsA, McsB, ClpC and whole operon were amplified using gene specific primers (Table S1). The size of the amplified product was reduced in mutant strain and corresponded to expected size of the genes. Figure S1 C KDa 175 90 60 40 30 20 10 ClpC protein Figure S1 C. Confirmation of in-frame deletion in mutant strains of Bacillus anthracis. Expression of ClpC (upper panel) and western blot developed using antiClpC antibodies (lower panel) using whole cell lysate of each mutant. GST is a glutathione S-transferase protein used as negative control. Figure S2 Verification of complemented strains of Bacillus anthracis by PCR. PCR was performed using specific primers for mcsB and clpC. Lane-1: DNA ladder (1-Kb); lane-2: mcsB gene amplification from genomic DNA of wild type B. anthracis Sterne; lane-3: mcsB gene amplification from genomic DNA of ΔmcsB strain; lane-4: mcsB gene amplification from mcsB complemented strain; lane-5: clpC gene amplification from genomic DNA of wild type B. anthracis Sterne; lane-6: clpC gene amplification from genomic DNA of ΔclpC strain; lane-7: clpC gene amplification from clpC complemented strain; and lane-8: DNA ladder (100-bp) Figure S3 A B Figure S3. continued… C D Phase contrast microscopy of wild type Bacillus anthracis Sterne and mutant strains. Cells were grown up to exponential phase in LB broth, diluted to OD595 = 0.035, plated on sporulation medium (in 3% low melting point agarose) and incubated at 30 °C. Time lapse imaging (1000 × magnification with oil immersion) was performed on phase contrast microscope (Nikon Ti Eclipse). Wild type (A); ΔmcsB (B); ΔclpC (C) and Δoperon (D). Figure S4. A B Scanning electron microscopy of vegetative cells of Bacillus anthracis. Cells were grown at 37 °C in LB broth and harvested at mid-log phase. Cells were washed with 0.1 M sodium phosphate buffer and fixed primarily with Karnovasky’s fixative and then treated with 1% osmium tetroxide. The samples were dehydrated, subjected to critical point drying and coated with gold. Cells were visualized under Zeiss EVO LS15. ΔclpC (A) and Δoperon (B). Table S1. List of primers used in this study Primer Name Primer sequence 5´→ 3´ Primers for knockout generation L CtsR Fp CCCTCAGAATGGTTGGAATTCATTCGTAGAGTGC (EcoR I) L CtsR Rp GATATTGCTCAATGATACTAGTTATATTTCTCATTTATCC (Spe I) R CtsR Fp CTTAGGGCTCGAATTCTATGCGCAATGTTAAG (EcoR I) R CtsR Rp GCTGATTTTCAAGATTACTAGTTTTATCCCTTACTTC (Spe I) L McsA Fp CTAAAGCAAGTTATTGAATTCAGTAATAATAATGTG (EcoR I) L McsA Rp CTTCTTCTCGTTGACTAGTTTTGTATAATG (Spe I) R McsA Fp GAACTAAAACTAGTTCTGAAACAATACG (Spe I) R McsA Rp GTTGAATAACACTAGTTAAATCTGCAATAATATC (Spe I) L McsB Fp GGGGATAGTGATGAATTCTCAAAACTGTAATATAAG (EcoR I) L McsB Rp CTTCATCCATGGACTAGTCGCTTCATTC (Spe I) R McsB Fp CACAACCAGGAATTCTACAACAATATG (EcoR I) R McsB Rp GATGGTTTTAAACTAGTCGATGCGTCAATAG (Spe I) L ClpC Fp GTTTTAAGTAGTCGAATTCGTTTGGC (EcoR I) L ClpC Rp CTTGAGATAAAGCTACTAGTTTCTGTGCTCTTTCTG (Spe I) R ClpC Fp GCCTTCCGTCCAGAATTCTTAAACCG (EcoR I) R ClpC Rp GATTACTACCATTTACTAGTAGACGATCGGCACGC (Spe I) L Operon Fp CCCTCAGAATGGTTGGAATTCATTCGTAGAGTGC (EcoR I) L Operon Rp GATATTGCTCAATGATACTAGTTATATTTCTCATTTATCC (Spe I) R Operon Fp GCCTTCCGTCCAGAATTCTTAAACCG (EcoR I) R Operon Rp GATTACTACCATTTACTAGTAGACGATCGGCACGC (Spe I) Primers for knockout confirmation CtsR Fp ATGAGAAATATATCTGATATCATTGAGCAAT CtsR Rp TTATTTATATTTCAGTGTTCTTAACATTGCGC McsA Fp ATGACTTGTCAAAACTGTAATATAAGACCAGC McsA Rp CTATTCCCCCTCTCTATACTCACTAAGC McsB Fp ATGTCACTGGACAAAATTATGAATGAAGCG McsB Rp TTAGTTTTTTTCAATACGTAATCGCTCACG ClpC Fp ATGATGTTTGGAAGATTTACAGAAAGAGCACAGAAAG ClpC Rp TTATTTTACCTTTTCGGCACTATGAATGACAAATG Primers for gene cloning pProExHTc-McsB Fp GAGAGGGGGAGGATCCCTATGTCACTGGACAAAATTATGAATG (Bam HI) pProExHTc-McsB Rp AGAAATCGCCTCAAGCTTGCGCTTAGTTTTTTTCAATACGTAATCGC (Hind III) pProExHTc-ClpC Fp GCAAGTAGGAGGGGATCCCTATGATGTTTGGAAGATTTACAG (Bam HI) pProExHTc-ClpC Rp GCCCTCTTAGTTTCTCGAGACTTATTTTACCTTTTCGGCAC (Xho I) Primers for complementation pYS5-SDM Fp GGCATTGTCTACGATACTAGTTTCAAGCACAGG (Spe I) pYS5-SDM Rp CCTGTGCTTGAAACTAGTATCGTAGACAATGCC (Spe I) pYS5-SDM Fp GGGGATTTTATGCGTGAGAATGGTACCGTCTATCCCG (Kpn I) pYS5-SDM Rp GGCAATGCCGGGATAGACGGTACCATTCTCACGCATA (Kpn I) ClpC Promoter Fp CCGAACACGGTACCTAAGCTCTCTAGCG (Kpn I) ClpC Promoter Rp ATCAGATACTAGTCTCATTTATC (Spe I) pYS5-McsB Fp GAATAGTTCTATGTCACTAGT CAAAATTATGAATG (Spe I) pYS5-McsB Rp CATCATAG AAATCGGATCCTACTTGCGCTTAG (Bam HI) pYS5-ClpC Fp GATTTCTATGATGTTTGG ACTAGTTACAGAAAGAGCA (Spe I) pYS5-ClpC Rp GCCCTCTTAGTTTGTGGATCCTTATTTTACC (Bam HI) Table S2. List of plasmids used in this study Name Description Resistance Marker Reference pSC Plasmid used for single crossovers in B. anthracis; AmpR in E. coli; EmR both in E. coli and B. anthracis Erythromycin, Ampicillin Andrei P. Pomerantsev, 2009 pSC-L-ctsR Left fragment of ctsR was cloned for first crossover Erythromycin, Ampicillin This study pSC-R-ctsR Right fragment of ctsR was cloned for second crossover Erythromycin, Ampicillin This study pSC-L-mcsA Left fragment of mcsA was cloned for first crossover Erythromycin, Ampicillin This study pSC-R-mcsA Right fragment of mcsA was cloned for second crossover Erythromycin, Ampicillin This study pSC-L-mcsB Left fragment of mcsB was cloned for first crossover Erythromycin, Ampicillin This study pSC-R-mcsB Right fragment of mcsB was cloned for second crossover Erythromycin, Ampicillin This study pSC-L-clpC Left fragment of clpC was cloned for first crossover Erythromycin, Ampicillin This study pSC-R-clpC Right fragment of clpC was cloned for second crossover Erythromycin, Ampicillin This study pSC-L-operon Left fragment of operon was cloned for first crossover Erythromycin, Ampicillin This study pSC-Roperon Right fragment of operon was cloned for second crossover Erythromycin, Ampicillin This study pCrePAS-71 Contains cre gene and strongly temperature-sensitive replicon for both E. coli and gram-positive bacteria; SpR in both E. coli and B. anthracis. Spectinomycin Andrei P. Pomerantsev, 2006 pYS5 Plasmid used for complementation in B. anthracis; Kanamycin, Ampicillin Yogendra Singh, 1989 AmpR in E. coli; KanR in B. anthracis pYS5-mcsB Complement plasmid expressing McsB under native promoter Kanamycin, Ampicillin This study pYS5-clpC Complement plasmid expressing ClpC under native promoter Kanamycin, Ampicillin This study pProExHTc E. coli expression vector with N-terminal His6-tag Ampicillin Invitrogen pProExHTcclpC Expression of His6-ClpC in E. coli Ampicillin This study pProExHTcmcsB Expression of His6-McsB in E. coli Ampicillin This study Table S3. Strains used in this study Name Resistance marker References E. coli B strain: F-, dcm, ompT, hsdS(rB- mB-), gal,λDE3(lacI lacUV5-T7 gene 1, ind1, sam7, nin5) - Invitrogen DH5α E. coli fhuA2, Δ(argF-lacZ)U169, phoA glnV44, Φ80, Δ(lacZ)M15, gyrA96, recA1, relA1, endA1, thi-1, hsdR17 - Invitrogen SCS110 E.coli SCS110 is an endA– derivative of the JM110 strain rpsL (Strr) thr leu endA thi-1 lacY galK galT ara tonA tsx dam dcm supE44 Δ(lacproAB) [F´ traD36 proAB lacIqZΔM15] - Stratagene B. anthracis strain pXO1+, pXO2- - NIAID, NIH 𝛥ctsR B. anthracis Sterne:: ctsR- - This study 𝛥mcsA B. anthracis Sterne:: mcsA- - This study 𝛥mcsB B. anthracis Sterne:: mcsB- - This study 𝛥clpC B. anthracis Sterne:: clpC- - This study B. anthracis Sterne:: clpC operon- - This study BL21(DE3) B. anthracis Sterne 34F2 𝛥operon Genotype mcsB complement B. anthracis Sterne:: mcsB- + pYS5-mcsB Kanamycin This study clpC complement B. anthracis Sterne:: clpC- + pYS5-clpC Kanamycin This study Detailed Materials and Methods Generation of B. anthracis Sterne clpC Operon Gene Mutants and their Characterization. To understand the role of clpC operon in the physiology of B. anthracis Sterne strain, the cre-lox genetic modification method was used to introduce precise genetic knockouts as reported earlier by Pomerantsev et al., (2006). In brief, the pSC vector was used to produce a deletion in each gene or whole operon (Figure S1 A) by two step recombination using the primers shown in Table S1. Plasmid pCrePAS was used for the elimination of DNA regions containing a spectinomycin resistance cassette located between two similarly oriented loxP sites. The deleted region of gene in each mutant strain was confirmed by DNA sequencing and PCR (Figure S1 B). The expression of ClpC protein in each mutant showed that all mutants had in-frame deletions (Figure S1 C). Whole Cell Lysate Preparation and Western Blot Analysis All mutant strains were grown at 37 °C for overnight and harvested at 12,000 × g for 10 min. Cells were suspended in sonication buffer [50 mM Tris-HCl (pH8.5), 5 mM βmercaptoethanol, 1 mM phenylmethylsulfonylfluoride (PMSF), 1× protease inhibitor cocktail (Roche Applied Science, USA) and 300 mM NaCl] and sonicated for 5 min. The lysed cells were centrifuged at 12,000 × g for 30 min. The supernatant was aliquoted and stored at 80 °C. Total protein in cell lysates were estimated using Bradford reagent and 25 μg of each lysate was loaded on 12% SDS-PAGE and transferred on nitrocellulose membrane (Millipore, USA) followed by blocking with 3% bovine serum albumin (SigmaAldrich, USA). Primary antibody against ClpC protein was raised in rabbit and used at 1:30,000 titer. HRP-conjugated secondary antibody against rabbit was used at 1:20,000 dilution. Blots were developed using Super-signal West Pico Chemi-Luminescent substrate (ThermoFisher Pierce, USA). Controls used were purified ClpC protein and GST protein. Complement Strain Preparation. Plasmid pYS5, a shuttle vector of E. coli and B. anthracis, has protective antigen gene under its native promoter (3). We created SpeI and KpnI restriction enzyme sites using Quick-change site-directed mutagenesis kit as per manufacturer’s instruction (Stratagene, USA) and primers (Table S1). SpeI restriction enzyme site was created within the signal sequence 39-bp downstream from the +1 ATG starting codon of protective antigen signal sequence while the KpnI restriction enzyme site created 297-bp upstream to the +1 ATG codon of PA signal sequence spanning the PA promoter region. Both the genes (mcsB and clpC) were amplified from the wild type genomic DNA with mcsB forward primer (SpeI), clpC forward primer (SpeI) and mcsB reverse primer (BamHI) and clpC reverse primer (BamHI). The promoter region of clpC operon were amplified from the wild type genomic DNA with forward primer (KpnI) and reverse primer (SpeI). The genes were cloned in the pYS5 (SpeI+BamHI digested) followed by the cloning of clpC operon promoter (KpnI+SpeI digested). The electrocompetent cells were prepared as described by Quinn and Dancer (1990). The plasmid containing mcsB and clpC genes were electroporated using BTX Electro cell Manipulator 600 (1KV, 186 ohms, 25µF using 0.1 cm Bio-Rad Electrocuvette) in SCS110 strain. The plasmids were isolated from SCS110 using Qiagen Miniprep kit (USA) and electroporated in respective knockouts electro-competent cells. The complementation was confirmed by PCR (Figure S2). Bacillus anthracis Spore Preparation. The wild type and knockout strains were grown in 10 mL Luria-Bertani (BD Difco, USA) broth up to mid-log phase (OD595 = 0.8). Each culture was inoculated into 100 mL sporulation medium containing 0.6 mM CaCl2.2H2O, 0.8 mM MgSO4.7H2O, 0.3 mM MnSO4.H2O, 85.5 mM NaCl, 0.025 mM ZnSO4, 0.02 mM CuSO4, and 8 g of LB broth/L (pH6.0) as described earlier (Barua et al., 2009). Cultures were incubated at 30 °C for 72 h on constant shaking at 200 rpm. The spores were harvested at 12,000 × g for 15 min at 4 °C and transferred to 50 mL autoclaved milliQ water to complete sporulation at 30 °C at 200 rpm. Spores were harvested at 120 h and washed thrice with autoclaved milliQ water and finally re-suspended in 5 mL milliQ water. Spores were heat activated at 65 °C for 30 min and stored at 20°C. Sporulation and germination efficiencies were calculated as described by Giebel et al., (2009) and Burns et al., (2010). Phase Contrast Time Lapse Imaging Bacillus mutant strains were grown in chemically defined media [62 mM K2HPO4, 44 mM KH2PO4, 15 mM (NH4)2SO4, 6.5 mM Sodium Citrate, 6.5 mM MgSO4, 2.2 mM Glucose, 6 μM L-glutamic acid, 7.5 μM MnCl2, 0.15 × Metal Mix, pH7.4] and diluted OD595 = 0.035. Sporulation medium supplemented with 1.5% high-resolution low-melting agarose pad was prepared on Corning Micro Slide Frosted (75 × 25 mm) with the help of AB gene-frame (17 × 54 mm). One μl of culture was spread on agarose pad sealed with ESCO cover slips No.1 thickness (24 × 60 mm). The cells were incubated at 30 °C for 24 h to 144 h in moist condition. Imaging was done at different time intervals on Nikon ECLIPSE TE 2000-S with phase III at 1000× magnification in oil immersion (Figure S3) (De Jong et al., 2011). Transmission Electron Microscopy. B. anthracis Sterne and deletion mutants were grown at 37 °C in LB Broth and harvested at mid log phase. The cells were pelleted at 12,000 × g for 10 min and washed three times with 100 mM sodium phosphate buffer (pH7.4). The samples were immediately transferred for primary fixation to Karnovasky’s fixative [2.5% Glutaraldehyde (TAAB, UK) + 2% Paraformaldehyde (SigmaAldrich, USA) in 100 mM sodium phosphate buffer pH7.4] for 12 h at 4 °C. The samples were rinsed thoroughly with sodium phosphate buffer to wash off the un-reacted excess fixative. Secondary fixation was performed with 1% osmium tetroxide (TAAB, UK) for 1 h at 4 °C and then dehydrated with graded acetone (Merck Chemicals, Germany) [30%, 50%, 70%, 80% (×2), 90%, 100% (×3); 30 min each at 4 °C]. Absolute xylene (Merck Chemicals, Germany) was used for clearing process and dehydrating agent was replaced from the samples. The bacterial samples were in-filtered and embedded into araldite resin mixture (TAAB, UK). Infiltration was carried out by gradually decreasing the concentration of clearing agent and increasing the concentration of embedding medium proportionately. Curing was processed at 55 °C for 24 h and then 65 °C for 48 h. Sectioning was performed with Leica UC6 ultra-cut and grids were observed in FEI Tecnai G2 Spirit at 200 KV (Putnam et al., 2013). Scanning Electron Microscopy. The deletion mutants and wild type strains were grown at 37 °C in LB broth and harvested at mid-log phase and processed as earlier described by Dubey et al., (2011). The cells were pelleted at 12,000 × g at 4 °C, washed three times with 100 mM sodium phosphate buffer (pH7.4). The samples were fixed with Karnovasky’s fixative (2.5% Glutaraldehyde + 2% Paraformaldehyde in 100 mM sodium phosphate buffer pH7.4) for 6 h at 4 °C and again washed with sodium phosphate buffer thrice. Secondary fixation was performed with 1% osmium tetroxide for 10 min at 4 °C and then dehydrated with graded ethanol [30%, 50%, 70%, 80% (×2), 90%, 100% (×3); 30 min each at 4 °C]. Samples were dried with a critical point drying technique and subjected to the gold coating of 10 nm thickness with an Agar sputter coater on alumimium stubs. Samples were observed in Zeiss Scanning Electron Microscope EVO LS15 at 20 KV. Comprehensive imaging, processing and analysis performed on Smart SEM software. Ni-NTA Protein Purification and Antibody Generation. The genes encoding for clpC were PCR amplified using B. anthracis Sterne genomic DNA, using primer pair pProEx-HTc-McsB Fp and pProEx-HTc-McsB Rp, pProEx-HTc-ClpC Fp and pProEx-HTc-ClpC Rp (Table S1). The amplicons thus generated were digested with BamHI and XhoI restriction enzymes respectively and ligated into pProEx-HTc previously digested with similar enzymes. The integrity of both plasmid constructs was confirmed by DNA sequencing. The recombinant His6-tagged proteins were purified by metal affinity protein purification. Escherichia coli BL21 (DE3) cells were transformed with pProExHTc-McsB and pProEx-HTc-ClpC plasmids expressing full-length proteins. The recombinant E. coli strains harboring the pProEx-HTc-McsB/ClpC plasmid was used to inoculate 1L of LB broth supplemented with ampicillin 100 𝜇g/mL followed by incubation at 37 °C with shaking (220 rpm) until A595 reached 0.8. The culture was induced with IPTG at concentration 1 mM and growth was continued for additional 1216 h at 16 °C. Cells were harvested at 10,800 × g for 10 min and stored at 80 °C. Pellets were thawed on ice and suspended in cell lysis buffer [50 mM Tris-Cl (pH8.5), 300 mM NaCl, 5 mM β-mercaptoethanol, 1 mM PMSF and 1× protease inhibitor cocktail (Roche Applied Science, USA)] and lysed by sonication. The cell lysates were centrifuged at 30,000 × g for 30 min. The supernatant containing recombinant protein was collected and incubated for 2 h with Ni2+-nitrilotriacetic acid resin (Qiagen, USA) pre-equilibrated with buffer [50 mM Tris-Cl (pH8.5), 300 mM NaCl, 10% glycerol, 20 mM imidazole, 10 mM β-mercaptoethanol and 1 mM PMSF]. After extensive washings with buffer A, resin was further washed with high salt containing buffer [50 mM Tris-Cl (pH8.5), 1 M NaCl, 10% glycerol, 20 mM imidazole, 10 mM β-mercaptoethanol, and 1 mM PMSF]. Elution was carried out in elution buffer [50 mM Tris-Cl (pH8.5), 150 mM NaCl, 10% glycerol, and 200 mM imidazole]. Protein fractions were run on 10% SDS-PAGE and stained with coomassie brilliant blue (Gupta et al., 2009). Purified fractions were pooled, dialyzed [20 mM Tris-Cl (pH8.0) 10% glycerol and 150 mM NaCl], aliquoted and stored at 80 °C. Rabbits were immunized with 500 g antigen in Freund’s complete adjuvant (SigmaAldrich, USA) at day one. Subsequently five booster doses of 200 g antigen in Freund’s incomplete adjuvant were given at 15th, 25th, 35th, 45th and 55th day. Serum was collected on 75th day and titer was determined by direct ELISA. Polyhydroxybutyrate Assay during Sporulation. Primary inoculum for PHB production was prepared using single bacterial colony from LB agar plate into 10 mL LB broth, at 37 °C for 1620 h at 200 rpm. It was used as inoculum in sporulation medium (0.6 mM CaCl2.2H2O, 0.8 mM MgSO4.7H2O, 0.3 mM MnSO4.H2O, 85.5 mM NaCl, 0.025 mM ZnSO4, 0.02 mM CuSO4 and 8 g of LB broth/L, pH6.0). PHB production was monitored in mcsB, clpC and operon deleted mutants and compared to B. anthracis Sterne as control. Cultures were grown in 200 mL sporulation medium by incubating at 37 °C and 200 rpm. Aliquots of 100 mL were analyzed for cell dry weight (CDW) and PHB content at various time periods upto 144 h after inoculation. Samples (100 mL) were centrifuged at 8,000 × g at 4 °C for 20 min. The pellet was washed with 10 mL saline solution (0.9 % NaCl). The pellet was dried at 85 °C for 36 h and weighed to estimate CDW. Cell pellet (40 mg) was processed and treated for propanolysis. Propyl-esters of β-hydroxyacids from PHB hydrolysis were analyzed by gas chromatograph (GC) equipped with dimethylpolysiloxane capillary column DB-1 (30 m × 0.25 mm × 0.25 µm) and flame ionization detector by the method described earlier (Patel et al., 2012). Assay of Anthrax Lethal Toxin in Supernatants. Wild type and deletion mutants were inoculated in 10 mL LB broth and incubated overnight at 37 °C. Secondary inoculation (10%) was performed in 50 mL Brain-Heart Infusion media (BD Difco, USA) containing 10% sodium bicarbonate. The cultures were incubated at 37 °C for 4 h at 200 rpm shaking. The cultures were pelleted at 12,000 × g for 30 min and supernatants were collected followed by their filter sterilization. Precipitation was performed by adding 20% trichloroacetic acid (Merck Chemicals, Germany) and incubating at 20°C for 1 h. Proteins were pelleted at 12,000 × g for 30 min at 4 °C. Protein pellets were washed thrice with 5 mL ice-chilled acetone. The pellets were dried at 95 °C and re-suspended in 1 mL PBS containing 1× protease-inhibitor cocktail (Roche Applied Sciences, USA). The resuspended protein pellets were loaded along with purified protective antigen/lethal factor on 12% SDS-PAGE followed by western blotting. References 1. Barua. S., McKevitt, M., DeGiusti, K., Hamm, E.E., Larabee, J., Shakir, S., et al. (2009) The mechanism of Bacillus anthracis intracellular germination requires multiple and highly diverse genetic loci. Infect Immun 77: 23-31. 2. Burns, D.A., Heap, J.T., Minton, N.P. (2010) SleC is essential for germination of Clostridium difficile spores in nutrient-rich medium supplemented with the bile salt taurocholate. J Bacteriol 192: 657-664. 3. De Jong, I.G., Beilharz, K., Kuipers, O.P., Veening, J.W. (2011) Live Cell Imaging of Bacillus subtilis and Streptococcus pneumoniae using Automated Timelapse Microscopy. J Vis Exp 53: e3145. 4. Dubey, G.P., Ben-Yehuda, S. (2011) Intracellular nanotubes mediate bacterial communication. Cell 144: 590-600. 5. Giebel, J.D., Carr, K.A., Anderson, E.C., Hanna, P.C. (2009) The germination-specific lytic enzymes SleB, CwlJ1 and CwlJ2 each contribute to Bacillus anthracis spore germination and virulence. J Bacteriol 191: 5569-5576. 6. Gupta, M., Sajid, A., Arora, G., Tandon, V., Singh, Y. (2009) Forkhead- associated domain-containing protein Rv0019c and polyketide-associated protein papA5, from substrate of serine/threonine protein kinase PknB to interacting proteins of Mycobacterium tuberculosis. J Biol Chem 284: 34723-34734. 7. Patel, S.K.S., Singh, M., Kumar, P., Purohit, H.J., Kalia, V.C. (2012) Exploitation of defined bacterial cultures for production of hydrogen and polyhydroxybutyrates from pea-shells. Biomass and Bioenergy 36: 218-225. 8. Pomerantsev, A.P., Camp, A., Leppla, S.H. (2009) A new minimal replicon of Bacillus anthracis plasmid pXO1. J Bacteriol 191: 5134-5146. 9. Putnam, E.E., Nock, A.M., Laeley, T.D., Shen, A. (2013) SpoIV and SipL are Clostridium difficile spore morphogenetic proteins. J Bacteriol 195: 1214-1225. 10. Quinn, C.P., Dancer, B.N. (1990) Transformation of vegetative cells of Bacillus anthracis with plasmid DNA. J Gen Microbiol 136: 1211-1215. 11. Singh, Y., Chaudhary, V.K., Leppla, S.H. (1989) A deleted variant of Bacillus anthracis protective antigen is non-toxic and blocks anthrax toxin in-vivo. J Biol Chem 264: 19103-19107.