Assay for detection of apoptosis by Annexin-V /PI staining

function of resolution. The displacement for an isotropic B-value is related to the displacement u by the equation B = 8;(u2). The isotropic B-value assumes equal movements in all the directions. However, the vibration of an atom need not be the same in all the directions, and in such a case motion is described by anisotropic displacement parameter. In this formulation the motion is described by an ellipsoid that can be rotated in any direction. The entire anisotropic displacement can be described in terms of six elements: UIJ, U22 and U33 specify the magnitude of movement in three axis and U 12, U t3 and U23 specify the rotation off the principal axis. Anisotropic displacement parameters can be converted to the isotropic equivalent by the formula Biso = 8;(Ull+l'22+U33). The B-values are restrained during refinement. Atoms that are bonded to each other influence each other's motion. B-values are restrained in such a manner that the average difference in the B-values of bonded atoms is kept to a target value. The B-values should vary smoothly along the protein chain and within the side chain. The usual target restraint for adjacent bonded main chain atom is 1.0 and for side chain the target value is 1.5 since one end of the side chain is free, ensuring the higher gradient. Similarly B-values can be graded for the one to three members of a bond angle. For main chain angles the target value is 1.5 and for the side chain angle the value is set to 2.0. Like rigid body refinement, it is done at the early stages of the refinement process. Refinement of the atomic B-factors is a bit tricky and is carried out in later stages of refinement.

The individual atoms were then refined by several cycles of conventional positional refinement, which uses the conjugate gradient minimization method. The proper weight term called Wa was calculated which was used for subsequent positional refinement (Brunger et al., 1987). In case of CNS this value was set to -1 and the program itself calculated these weights. The refinement was started using data in the range 50 A -4.0 A and higher resolution data were added in a stepwise fashion. After complete data had been added, the F0-Fc and 2F0-Fc electron density maps in addition to the composite omit map were calculated and displayed on an HP xw8400workstation (Hewlett-Packard Company, U.S.A.) using Coot (Emsley P, 2004 ). The electron density map was examined in the context of the model and the regions of the map where the electron density was not satisfactory or the model did not fit the density were identified. Using Coot, the residues were mutated to the sequence of the molecule of interest and wherever required, moved locally to correspond to the visible density. This was followed by refinement to check if the changes made could be accepted or not. Depending on the resolution to which X-ray data was available, anisotropic or individual B-factors were also refined. This process of model building and refinement was carried out iteratively until all the differences in sequence with the probe model had been accounted for and there was no ambiguity in the fit between the model and the electron density. Water molecules were included in the model using the 'water pick' program available in CNS only after a sufficient level of refinement had been achieved. This was followed by visual examination of the waters to avoid inclusion of spurious water molecules. The B-value is the measurement of the displacement of an atom from thermal motion, conformational disorder and static lattice disorder. This vibration will smear out the electron density and will also decrease the scattering power of the atom as a

sum runs over all the reflections in your data set, and k is a scale factor needed to put the Fe on the same scale as the Fobs· A model consists typically of five parameters for each atom: x,y,z, B, and Q. The triplet (x,y,z) specifies the position of each atom in an orthogonal coordinate system. B is the B-factor or temperature factor of each atom, and it is related to the thermal motion of the atom. B-factor also contains information about other types of "disorder" including errors that you are being made while constructing and refining model. Q is the occupancy and it is the fraction of time that the atom spends at position (x,y,z). Typically, Q=l. If one has data better than about 1.8 A, then occupancies between zero and one are sometimes used. Refinement procedures for antibodies involve two basic procedures, rigid body refinement followed by positional refinement. Rigid body refinement is used to refine the results obtained from MR in terms of orientation and position of the starting model in the unit cell. Positional refinement is used to refine the positions of individual atoms in space. Both conventional R-factor (Rcryst) and the free R-value (Rfree) (BrUnger, 1992) were used to monitor the progress of refinement. 10% of the reflections were set aside at random to monitor the Rfree during refinement. Rigid body refinement was carried out to further refine the positioning of the probe molecule in the target unit cell. The probe models that gave the highest correlation coefficients were thus subjected to rigid body refinement. Refinement was initially done using data in the range of 50 A -4 A; thereafter data up to the maximum available resolution were added in a step wise manner. The Fab molecule can be defined as an assembly of four domains, the VH, VL, CH and CL. Consequently, rigid body refinement where these domains were considered as discrete rigid units was carried out.

This section describes the detailed refinement strategies used for structure determination. The structures presented in the thesis were refined using CNS (Brunger, 2007; Brunger et al., 1998). The refinement of structures obtained after molecular replacement was done using Crystallography and NMR system (CNS) suite of programs (BrUnger et al., 1998) based on the refinement of crystal structures using Cartesian (BrUnger et al., 1987) or torsion-angle molecular dynamics (Rice and BrUnger, 1994). This task file automatically computes a cross-validated crA estimate, determines a weighting scheme between the X-ray refinement target function and the geometric energy function, refines a flat bulk solvent model (Jiang and Brunger, 1994) and an overall anisotropic B-value of the model by least squares minimization, and subsequently refines the atomic positions. Available target functions include the maximum-likelihood functions MLF, MLI and MLHL (Pannu et al., 1998). Refinement is an iterative process in which the atomic model is modified, structure factor amplitudes are calculated from the modified model, and the agreement between these calculated structure factor amplitudes (IFcl) and the experimental or observed ones (IF ~bsD is determined. The goal is to find the model that produces the best agreement between lfohsl and lfcl. Refinement is a problem of finding the minimum of a function that mathematically expresses the agreement between IFobsl and lfcl. This function is called a target function. A commonly used target function is the crystallographic residual: SUM {(IFobsl -k1Fcl)2}, where the

Structure refinement using the Crystallography and NMR system (CNS) suite

A control reaction was done with the control annealed DNA lacking the oligonucleotide. The constituents were mixed and incubated on ice for 2 min. afterwards, at room temperature, for 5 min. The reaction was further carried out at 37 °C for 2 h followed by heating at 70 °C for 10 min. 12.5 J.tl of the reaction products were analyzed on an agarose gel along with annealed samples to check the complementary strand synthesis. The samples were diluted I 0-times with water and 5 J.ll of the diluted sample was used to transform 50 J.ll of E. coli host strain, DH5a cells. The suspension was pl~!ed on 2 LB agar plates containing ampicillin. Single colonies were picked, grown in liquid culture and miniprep screening of DNA was done to select the positive clones.

Annealed DNA 10.0 J.ll I OX synthesis buffer 2.5 J.ll 1 OX ligation buffer 1.0 J.ll dNTP mix (100 mM) 1.0 J.ll ATP (100 mM) 0.25 J.ll ~ T7 DNA polymerase (5 U/J.tl) 0.5 J.ll T4 DNA ligase (400 U/J.tl) 0.5 J.ll H20 9.25 J.ll Total 25.0 J.l

Titration of uracil containing template: The crude preparation of the phagemid DNA (1 ml aliquot), was used to titrate the uridine incorporation in the template. The strains CJ236 (ung-duf) and DH5aF'(ung+ dut+) of E. coli were transformed with the diluted template DNA The CJ236 cells, plated in the presence of ampicillin and chloramphenicol while DH5aF' cells, plated in the presence of ampicillin alone, were grown overnight on LB agar plates. The good incorporation of uridine gave no colonies or very few colonies in DH5aF' cells whereas with CJ236 several colonies were obtained. A ratio of 103-104 between the number of colonies in CJ236 to that in DH5aF' cells was considered ideal for an efficient incorporation of uridine. Phosphorylation of the mutagenic oligonucleotide: The components of a standard reaction to carry out the phosphorylation are described below Oligonucleotide (180 nmoVml) 1.0 J.ll 1 OX Kinase buffer 2.5 J.ll 10mMATP 1.0 J.ll 10 mM spermidine 0.25 J.ll 100mMDTT 1.25 J.ll T4 polynucleotide Kinase 0.5 J.ll H20 18.5 J.ll Total 25.0 J.LI The constituents were . mixed thoroughly, incubated at 37 °C for 30 min. and subsequently, the enzyme was denatured by heat inactivation at 70 °C for 10 min. Annealing of the mutagenic oligonucleotide: 750 ng (approximately) of the uracil containing single stranded template and 1 J.L) of the phosphorylated· oligonucleotide were taken in IX annealing buffer making up the total reaction volume 20 J.LI. A control reaction, was also carried out simultaneously, lacking the oligonucleotide. The contents were mixed by vortexing and incubated at 95 °C for 10 min. in a water bath. The reaction mixtures were further incubated at 80 °C for I 0 min. in a heat block and the heat block was transferred to ambient temperature, cooled slowly to about 30 °C over a period of 30-60 min. Complementary DNA strand synthesis: The oligonucleotide annealed uracil containing template was used for complementary strand synthesis in the following reaction.

Site-directed mutagenesis was done according to the method employed by Kunkel et al., 1987. Preparation of Uracil containing phagemid: E. coli strain CJ236 was transformed with the required template DNA and grown on LB plates containing the antibiotics, ampicillin 100 Jlg/ml and chloramphenicol 30 Jlg/ml (stock solution made in alcohol). Further, the plates were incubated at 37 °C for 12 h and a single colony was picked from the center of the plate, inoculated in 5 ml LB containing ampicillin and chloramphenicol. The liquid culture was grown at 37 °C overnight with vigorous. shaking. About 500 Jll of the culture was diluted 40-times with LB containing ampici11in and chloramphenicol and grown at 37 °C with vigorous shaking (200 rpm) upto an OD600 of 0.25-0.3. The speed of shaker was reduced to 100 rpm and the culture was left for 30 min. for the F pilus to grow. Afterwards, it was infected with VCS Ml3 helper phage at an MOl of 1:20. The cells were grown for 30 min. in a stationary culture to allow the phages to infect, followed by slow shaking ( 100 rpm) for one hour. Subsequently, the culture was diluted 10-times with 2X YT medium containing ampicillin and chloramphenicol and grown in the presence of 0.25 Jlg/ml uridine and 50 Jlg/ml kanamycin at 37 °C overnight with vigorous shaking. The following day, the culture was chilled on ice for 10 min. and centrifuged at 12,000 rpm for 10 min. at 4 °C in a Sorvall RC5C centrifuge using a GSA rotor. The pellet was discarded and the supernatant was centrifuged again in fresh GSA bottles. A small aliquot of about 1 ml from the supernatant was saved for titration and the . precipitation of the single stranded phagemid was carried out using 0.15 volume of 16.67% PEG in 3.3 M NaCl followed by incubation on ice for 4 h. J'he mixture was centrifuged at 12,000 rpm at 4 °C for 30 min. using a GSA rotor and the pellet was resuspended in 3 ml TE buffer. The suspension was centrifuged at 15,000 rpm at 4 °C for 10 min. using a SS34 rotor. The supernatant was ultracentrifugated at 100,000 g at 4 °C for 2.5 h. The pellet was resuspended in 500 Jll TE buffer followed by phenol-chloroform extraction and precipitation of the single stranded DNA with ethanol for 30 min. at -70 °C. The DNA pellet was washed with 70% ethanol, dried and dissolved in 200 Jll TE buffer. The uracil containing template was quantitated by analysing on an agarose gel.

Site-directed Mutagenesis

Human oocytes were washed twice with PBS containing 0.1 % BSA and then incubated with 1 :50 dilution of immune or pre-immune serum samples at RT for 30 min. Following washing with PBS (3 changes of 5 min each), the oocytes were treated with goat anti-rabbit Ig-FITC conjugate for 30 min at RT. After washing with PBS, the treated oocytes were mounted in Glyceroi:PBS (9: 1) and examined under fluorescent microscope.

Indirect Immunofluorescence on Human Oocytes

For analysis of viral DNA by dot blot, I X I o5 cells were seeded in each we11 of the 9~ well plate and infected in duplicate with 50 J.Ll of the plaque pick for I h, followed b: addition of 50 J.Ll of CM to each well. Infected cells were incubated for 5 days, afte which the culture supernatant was saved and ce11s were processed for dot blot analysi~ Ce11s were lysed with 200 J.LI of 0.5 M NaOH. The alkali was neutralized by addition o 50 J.LI of 4 M ammonium acetate. The nylon membrane was wetted in warm water an( washed in dot blot solution (1 M ammonium acetate, 0.02 N NaOH) and the cell lysatt was blotted on to the membrane using a dot blot apparatus (Bio-Rad), dried, UV eros: linked and processed for prehybridization and hybridization. For the isolation of total genomic DNA, cells infected in a 35 mm culture dish wen harvested 72 h post infection (pi) and treated with 400 J.LI of DNA extraction buffer(]( mM Tris HCI, pH 8, 0.6% SDS, 10 mM EDTA)·and 50 J.Ll of 20 mg/ml proteinase K a 37°C for 12-I6 h. The DNA was extracted twice with phenol:chloroform:isoamy alcohol (25:24: 1) and once with chloroform. For each extraction, the suspension wa! mixed by inverting the eppendorf and separated by centrifugation at 2,000 rpm for 3 mir in a microfuge. DNA was precipitated with I ml of 95% ethanol at -20°C for 4 h anc pelleted at 4,500 rpm for 20 min. The pellet was washed with 70% ethanol, dried anc resuspended in 50 J.LI of TE. DNA was digested with Hind III, resolved on a 0.8% agarose gel and processed for Southern blotting. Positive clones were amplified b) infecting cells at a multiplicity of infection (MOl) of ~1 for 10 days and the amplifiec virus. was titrated using a plaque assay. Sf9 cells were infected at -I 0 MOl fo1 expression of the r-proteins.

Screening of the Recombinant Viruses

E. coli strains deficient in specific proteases were used to study their influence on the expression of r-bZP3. BL21 (DE3) and BL21 (pLysS) deficient in ompT and ion proteases and DF5 carrying a targeted mutation of the ptr gene, were transformed with the pQE-bZP3 plasmid. Colonies obtained were grown 0/N and subcultured next morning and grown till A6oo=0.7. Cultures were then induced with 0.5 mM IPTG for 3 h. Harvested cells were checked by SDS-P AGE and immunoblotting.

Expression of r-bZP3 in Different E. coli Strains

centrifuged at 10,000 rpm for 10 min, washed with 70% ethanol and dried. DNA was resuspended in 500 J..Ll of TE containing 20 J..Lg/ml RNAase, incubated at RT for 30 min and analyzed by agarose gel electrophoresis. DNA for transfection was prepared using the Plasmid midi kit DNA purification system using protocols described in the manual.

A 1000 ml culture of cells harboring the plasmid were grown 0/N in LB Amp· Next morning the culture was chilled and cells pelleted at 4,500 rpm in a Sorvall SS34 rotor for 20 min. The supernatant was discarded and cells were washed with 100 ml of STE buffer (0.1 M NaCI, 10 mM Tris HCl and 1 mM EDT A, pH 8.0). The pellet obtained after centrifugation was resuspended in I 0 ml of GTE solution containing I mg/ml lysozyme and the mixture was incubated at RT for 20 min at 4oc. Alkaline SDS (20 ml) was added and the mixture was incubated at RT for 10 min after mixing gently by inverting the tube. Ice cold potassium acetate solution ( 15 ml) was added and the tube was chilled on ice for 15 min and then centrifuged at 18,000 rpm at 40C in a SS34 rotor. The supernatant was carefully transferred to a fresh tube, DNA was precipitated by adding 0.6 volume isopropanol and incubating at RT for 10 min and then recovered by centrifugation at 5000 rpm at RT for 30 min. DNA was rinsed with 70% ethanol, dried and dissolved in 3 ml of TE. To the nucleic acid solution 3 ml of chilled LiCI (5 M) was added, mixed and the precipitate removed after spinning at 10,000 rpm for 10 min at 40 C. DNA was precipitated from the supernatant using an equal volume of isopropanol,

Large Scale Plasmid DNA Isolation

a 1.5 ml eppendorf tube and the gel slice put into the paper cone. The tube was centrifuged for 10 minutes at room temperature, to elute the DNA into the filtrate. The filtrate was extracted with one volume of phenol I chloroform ( 1:1 vlv ) , and the DNA precipitated from the aqueous phase by the addition of 5 M NaCl to a final concentration of 1 M, and 2 - 3 volumes of ethanol at -20°C, for a few hours. The centrifuged DNA pellet was dissolved in an appropriate volume of TE.

After digestion of the plasmid DNA with appropriate restriction enzymes, the DNA fragments were resolved by electrophoresis on preparative agarose gels of a suitable percentage, and stained with ethidium bromide as described above. Depending upon the amount of DNA to be resolved on the gel, the size of the sample well varied from 1.5 em - 5 em x 0.3 em, such that the desired fragment could be cut out with a minimum of agarose accompanying it. The DNA bands were visualised under long wave UV ( 366 nm ), using a hand held monitor model UVGL-58 Mineralight Lamp, UVP, Inc., California, USA), and the desired fragment cut out as a thin agarose slice keeping the size of the slice as small as possible ) . DNA was eluted from the agarose slice by the method of Zhu et al., ( 1985). Briefly, a GeneScreen ( NEN ) or Durapore ( Millipore, GVWP 04 700 membrane was wetted with 200 ul of elution buffer ( 0.1 % SDS +50 mM Tris. HCl, pH 7.5 ), and folded over to form a cone. Meanwhile, the conical lower half of an eppendorf tube was cut off and a hole pierced in the bottom with a hot wire or needle. The membrane was placed into this cone, pushing it as far as possible. This assembly was then transferred to

Isolation of restriction fragments of DNA

32p -dCTP specific activity 400 or 800 Ci 1 mmole was from Amersham, UK or from New England Nuclear division of DuPont, USA. 125I was from Amersham.

Radioactive chemicals.

The inhibition potency of our synthetic substrate, lactal (31), was determined by measuring the hydrolytic activity of ~-D-galactosidase on o-nitrophenyl ~-D­galactopyranoside.97 Each assay tube contained 2 ml of o-nitrophenyl ~-D galactopyranoside solution (500 IlM), 0.25 units of ~-D-galactosidase (source: Aspergillus oryzae; purchased from Sigma, cat. no. G-5160) and a certain concentration of lacta!. The tube was incubated at 30°C for 13 min, after which 200 III of the mixture was added to a tube containing 100 III of acetate buffer (25 mM, pH = 4.5) and 200 III of sodium carbonate solution (200 mM). The colour liberated was read spectrophotometrically at 400 nm. The control tube contained everything except the substrate, lacta!.

~-D-Galactosidase inhibition by Lactal

The Luria Bertani (LB; pH 7.5) medium was prepared in double distilled water by adding, NaCl 1%, Yeast extract 0.5%, and Tryptone 1% and sterilized by autoclaving under pressure (15 lbslinch2) for 20 min. Solid growth medium was prepared by adding 1.5% agar to LB prior to autoclaving. Appropriate antibiotics were added after cooling the medium to approximately 50-60°C. Bacterial cultures were grown in LB medium at 37°C in an orbital shaker set at 200 revolutions per minute (rpm).

Media composition and bacterial culture

Phagocytesfromtheheadkidneywerestimulatedwithphorbol12-myristate13 -acetate(PMA,SigmachemicalCo)andtherespiratoryburstwasdeterminedbytheluminol-enhancedCLmethod(ScottandKlesius,1981)

AcidphosphatasewasassayedfollowingtheprocedureofMorton(1955).Theactivityoftheenzymewasexpressedaspmolphenolformedmin'1mg'1protein.

Acidphosphatase(ACP:acidorthophosphoricphosphohydrolase)(EC3.1.3.2)

Meancorpuscularhaemoglobinconcentration(MCHC)istheaverageHbconcentrationperunitvolume(100)ofpackedredcells(W/V).Henceitisexpresseding/1whichisthesameaspercent(%).ItiscalculatedbythefollowingformulaHbMCHC=—......x100(g/dl)PCV

MCHC

MeancellVolume(MCV).Itisexpressedinfentolitres(1fentolitreorflisequivalentto10'151)andcalculatedby thefollowingformula:PCVMCV=.....................x10(fl)RBC8.10.6.2.MCHMeancellhaemoglobin(MCH)=AverageweightofHbinanerythrocyte.Itisexpressedinpicograms(pg)whichisequivalentto10"12g.Itiscalculatedbythefollowingformula:HbMCH=-----------------x10(ppg)RBC

MCV

RedBloodcellsindices

Thefishessurvivedwithoutanymortalityintheeffluentconcentration ofnominalvalues2%,5%and7%.The30,60,90and120dayschronicexposurewith20fishaddedrandomlytoeachof60by40by240cmplastictankswasbegunwithfishfromthesameoriginastheseandintheinitialacutebioassays.Flowratesmaintainedtothetanksallowedfor twovolumesturnovers24hr.

Thefisheswereexposedtodifferentconcentrationsofeffluentandthenumberoffishineachconcentrationwasrecorded.Thedataweresubjectedtoprobitanalysis(Finney,1964)andDragstedtandBehven’sequation(Carpenter,1975)todetermineLC50values.Apresumableharmlessconcentration(C)oftheeffluentwasalsocalculatedbyusingthesafefactororapplicationfactor(Sprague,1971)employingtheformulaC=Where,48hrLC50xAS24 hrLC50S= -------------------48hr LC50A=0.3(constant)Thesafeconcentrationisausefulunitofmeasurementofacceptableamountoftheeffluent,whichhasnolethalityandstresstotheanimalexposed.Approximately1/3ofLCsoofvalueofeffluentwasselectedassublethalconcentrationinthepresentstudy.Fishesweredividedinto4groupsandkeptin401glassaquariacontaining wellwaterofpH7.2.GroupI,IIandIDwerekeptin2%,5%and7%ofeffluents(Figure7)respectivelyandexposedto24,48and72(short-term)periods.Allacutelethalitytestswereconductedaccordingtothe methodsofthe AmericanPublicHealthAssociation(1985).GroupIVservedascontrol.

Bioassay

polymerase and [a-32p] UTP (specific activity 3000Ci/mmole). The Riboprobe in vitro Transcription Systems (Promega) was used to make the in vitro transcripts. According to the manufacturer's directions, 0.2-lpg of the linearized DNA template was combined with the following components, in a final volume of 20pl, at room temperature in the following order: 4pl of SX transcription buffer (200mM Tris-HCl, pH 7.5, 30mM MgCh, lOmM Spermidine, 50mM NaCl), 2pl of lOOmM DTT, 20U of RNasin Ribonuclease inhibitor, 2.5mM each of ATP, GTP and CTP (pH 7.0), 2.4pl of lOOpM UTP (pH 7.0), Spl (50pCi at lOpCi/pl) of [a-32P]UTP and 15-20U of T7 or SP6 RNA Polymerase. For carrying out cold in vitro transcription all the four nucleotides (ATP, GTP, CTP, and UTP) were added at 2.5mM concentration and the reaction volume was made up with nuclease free water. The mixture was incubated at 370C for 60 min. The reaction was stopped using the stop buffer (50mM Tris-Cl, pH 7.5, SmM EDTA, 25pg tRNA/ml) and chilled on ice. RQl RNase-free DNase was added at a concentration of lU/pg of template DNA and incubated at 370C for 15 min to remove the DNA template following transcription. The transcripts were then purified by phenol : chloroform : isoamyl alcohol and chloroform : isoamyl alcohol extractions, followed by precipitation with 2.5 volumes of absolute alcohol and 0.5 volumes of 7.5M ammonium acetate and then 0.5 volumes of 1M ammonium acetate to remove the unincorporated nucleotides. After centrifugation for 30 min at 13,000 rpm the supernatant was carefully removed. The pellet was washed with 70% ethanol, vacuum dried and dissolved in 20pl of NFW

Plasmids containing the ribozymes or substrates were linearized at their 3' end with the appropriate enzymes. The linearized DNA was purified using the Qiagen Gel Extraction kit as described before (section 7.9). In vitro transcription reaction was then carried out using both T7 or SP6 RNA

In vitro Transcription:

Oligonucleotides used in this study were chemically synthesized by Sigma-Genosys (The Woodlands, TX, U.S.A.).

Oligonucleotides

DTT. Then contents were then mixed and 1μl (200 units) of M-MLV was added. The mixture was then incubated at 37°C for 50 minutes. The reaction was stopped by incubating the mixture at 70°C for 15 minutes. The cDNA thus prepared was then used as a template for PCR. The expression of the investigated genes was determined by normalizing their expression against the expression of actin or GAPDH gene

Semi-quantitative RT-PCR

μg of total RNA was reverse-transcribed using poly-T oligonucleotide and M-MLV reverse transcriptase (Invitrogen) according to manufacturer’s protocol. Briefly, a 20μl reaction volume was made for 1μg of RNA. In a microcentrifuge tube, 1μl oligo (dT)(500μg/ml) , 1μg total RNA, 1μl 10mM dNTP mix and sterile water was added to afinal volume of 13μl. The mixture was then incubated at 65°C for 5 minutes ad quickly chilled on ice. To this mixture were added 4μl of 5X first strand buffer and 2μl of 0.1M

Activation of H50 protein chip array

b. 5 μl of ACN + TFA (25% ACN in PBS + 0.1% TFA) was added to the spot surface and removed after 30 sec. c. 5 μl of cell lysate sample was then spotted on the chip and kept in a humid chamber for 30 min. d. Stringent washes were given by spotting 5 μl water on the spot surface for 30 sec and removing using Whatman filter paper strips. This was followed with a 25% ACN wash or three washes with 25% ACN or 50% CAN or 75% ACN. e. Washing was performed by spotting 5 μl of water for 30 sec followed by removal using Whatman filter paper strips. f. Dried chip at room temperature. g. 1-2 μl of SAP matrix (5 mg of matrix + 200 μl ACN + 200 μl of 1% TFA) was then spotted on the chip surface and allowed to dry. h. The chip was then placed in the SELDI machine

5 μl of water was added to each spot on the chip and removed after 30 sec using Whatman filter paper strips. Care was taken not to touch the spot surface. This step was repeated once

Typically, 100-200 ng of DNA was used in each ligation reaction. The ratio of vector to insert was maintained between 1:3 and 1:5. The reactions were usually done in a 10 μl volume containing ligation buffer (provided by the manufacturer) and 0.05 Weiss units of T4 DNA ligase, at 16°C for 12-16 hr

Ligation of DNA

NP-40 1% Tris 50 mM Sodiun deoxycholate 0.5% SDS 0.1% pH adjusted to 8.0 Running buffer for Western blotting Glycine 14.4g/l Tris base 3.05g/l SDS 1.0g/l Transfer buffer for western blotting Glycine 14.4g/l Tris base 3.03g/l The above salts were dissolved in 800ml of miliQ water and 200ml of methanol was then added. The buffer was chilled before use. PBST for Western blot 10X PBS (1000 ml) Sodium chloride 80 g Potassium chloride 2 g Disodium hydrogen phosphate 14.1 g (Na2HPO4) Potassium dihydrogen phosphate 2.49 g (KH2PO4) 1 l of 1X PBS + 1 ml of Tween-20

TBF-I buffer (200ml) Potassium acetate 0.588 g Calcium chloride 0.249 g Manganese chloride 1.98 g Rubidium chloride 2.418 g 15% Glycerol 30 ml pH adjusted to 5.8 with 1M acetic acid TBF-II buffer (100 ml) MOPS 0.209 g Calcium chloride 1.102 g Rubidium chloride 0.120 g 15% Glycerol 15 ml pH adjusted to 6.5 with 1M potassium hydroxide Acrylamide solution (30%) Acrylamide 29 g Bis-acrylamide 1 g H2O 100 ml Non denaturing polyacrylamide gel (12%) 30% acrylamide 38.6 ml H2O 40.6 ml TBE 20 ml 10% APS 0.7 ml RIPA buffer (Radio Immuno Precipitation Assay buffer): RIPA buffer for bacterial cell lysis Sodium chloride 150 mM

Water to 1000 ml MacConkey lactose agar: MacConkey Agar Base (Difco) 51.5 g Lactose 1% Water to 1000 ml Maloy agar: Tryptone 5 g Yeast extract 5 g NaCl 10 g NaH2PO4 10 g Chlorotetracycline (12.5 mg/ml) 4 ml Water 1000 ml Bacto-agar 15 g After autoclaving, the following solutions were added, ZnCl2 (20 mM) 5 ml Quinaldic acid (10 mg/ml) 10 ml Citrate buffer: (0.1 M; pH 5.5) Citric acid (0.1 M) 4.7 volumes Sodium citrate (0.1 M) 15.4 volumes TBE and TAE buffers: TBE: 90 mM Tris-borate, 2 mM EDTA (pH 8.0) and TAE: 40 mM Tris-acetate, 2 mM EDTA (pH 8.0) were used as standard electrophoresis buffers. TBE and TAE were prepared as 10X and 50X concentrated stock solutions, respectively, and used at 1X concentration

cto-agar 15 g LBON agar: LBON medium1000 mlBacto-agar 15 gLB soft agar: LB medium 100 ml Bacto-agar 0.6 gK-Medium: KH2PO4 1.0 mM FeSO4 0.5 mg/l (NH4)2SO4 1.5 mM MgCl2 0.08 mM Casamino acids 5 g/l Thiamine 2 mg/l pH was adjusted to 7.0 with Tris free base. K-medium is low osmolarity (70 mOsm) medium (Kennedy, 1982). Z broth: LB medium 100 ml CaCl2 (0.5 M) 0.5 ml MacConkey agar: MacConkey Agar (Difco) 51.5 g Water to 1000 ml MacConkey galactose agar: MacConkey Agar Base (Difco) 51.5 g Galactose 1%

Glucose/Glycerol-minimal A 19 amino acid medium: This medium is essentially the same as glucose/glycerol-minimal A medium described above except that all the 19 amino acids (except tryptophan) were added after autoclaving in a final concentration of 40 μg/ml from autoclaved 4mg/ml amino acid stock solutions. Minimal agar: Contained 1.5% Bacto-agar (Difco) in minimal A Medium. The plates were poured after mixing double strength minimal A medium with 4% agar (in water) that had been autoclaved separately. Wherever required, to test polaity relif at lacZ(am) or trpE(fs), meliobose (0.2%) was replaced for glucose and anthranilate at 100 μg/ml (4 mg/ml stock prepared in DMF) was replaced for tryptophan respectively. LB medium: Tryptone 10 g Yeast extract 5 g NaCl 10 g Water to 1000 ml pH adjusted to 7.0 - 7.2 with 1 N NaOH. LBON medium: Tryptone 10 g Yeast extract 5 g Water to 1000 ml pH adjusted to 7.0 - 7.2 with 1 N NaOH LB agar: LB medium 1000 ml

All the media and buffers were sterilized by autoclaving for 15 minutes at 121°C. Media and buffers used in this study are described below. Glucose/Glycerol-minimal A medium: K2HPO4 10.5 g KH2PO4 4.5 g (NH4)2SO4 1 g Sodium citrate, 2H2O 0.5 g Water to 1000 ml After autoclaving the following solutions were added. MgSO4 (1 M) 1 ml Glucose (20%) 10 ml Or Glycerol (80%) 5ml Vitamin B1 (1%) 0.1 ml Amino acids and bases, when required, were added to a final concentration of 40 μg/ml. When growth on other carbon sources was to be tested, glucose was substituted by the appropriate sugar at 0.2%; when used as carbon source, the final concentration of Casamino acids was 0.5%

Media and buffers

s promastigotes develop from procyclic to metacyclic forms, the surface LPG undergoes changes in size and carbohydrate structure. Procyclic promastigotes express a smaller LPG capable of binding to the sand-fly midgut, while metacyclic promastigotes express a larger LPG typically accompanied by changes in the terminal sugar of some of these units (McConville et al., 1992). The lectin peanut agglutinin (PNA) binds to terminal galactose of procyclic LPG but does not bind its metacyclic LPG counterparts which terminate in arabinose. This principle is used in assessing the number of metacyclics in a culture (Sacks et al., 1985). Briefly, after appropriate incubation, 107 cells were harvested and washed once with PBS followed by resuspension in 1mL PBS. PNA (1mg/ mL, prepared in PBS) was added to the cells at a final concentration of 10011g/ mL and incubated at 23°C for 1hr followed by incubation on a shaker incubator set at 40rpm for 5 min. The clumps formed were then pelleted at 100 x g for 3 min at RT. From the supernatant, 1011L was withdrawn for counting on a Neubauer's chamber to get the number of metacyclics per 107 cells

Assay for measuring the number of metacyclic parasites (Peanut Agglutination Assay)

RNA was isolated as described above. 3'RACE was carried out using a kit procured from Invitrogen (Carlsbad, CA) according to manufacturer's instructions. Briefly, 4~-tg of RNA was taken and e-DNA prepared using adaptor primer (AP) provided in the kit. This e-DNA was then used as template in a PCR reaction using a gene specific forward primer (Ld30RA3 and Ld34RA1), and the abridged universal amplification primer (AUAP) that is homologous to the adaptor primer as the reverse primer. The PCR product generated was then sequenced using T7 an SP6 primers after cloning into pGEM-TEasy vector as described below

Rapid Amplification of e-DNA ends (RACE)

x g for 10 min at RT. The supernatant was centrifuged at 1258 x g for 10 min at RT. The pellet obtained was washed 2X at 4°C in half the culture volume of Cytomix buffer (120 mM KCl, 0.15 mM CaCh, 10 mM K2HP04, 25 mM HEPES, 2 mM EDTA, and 2mM MgCh; pH 7.6) and then resuspended in chilled cytomix buffer at a density of 2 X 108 cells/mL. Electroporation: For a single electroporation, 2011g of plasmid (in water or 10mM Tris pH 8.0) for episomal expression and 5Jlg of plasmid for integration events, was added to a pre-chilled cuvette ( 4mm, BTX, San Diego, CA). 500J1L of chilled cell suspension (108 cells) processed as above was transferred to the cuvette and mixed with DNA by gently tapping and incubated on ice for 10 min. The cells were electroporated twice at 25 J.IF, 1500 V (3.75 kV /em), pausing 10 s between pulses (Robinson and Beverley, 2003) in a BioRad Gene Pulser X Cell electroporator. The cell suspension was then transferred to 5mL of mDMEM containing 20% FBS and allowed to recover for ~18hrs before antibiotic selection commenced. Selection of transformants: Selection of parasites containing recombinant DNA was carried out initially in liquid medium followed by culture with agar. After the rest period, the electroporated cells were exposed to 1011g/ mL of G418 or Hygromycin B for 48 hrs with antibiotic being increased to 2011g/ mL and 50Jlg/ mL at 48 hr. intervals. Part of the cells were then plated onto freshly poured mDMEM plates (1X mDMEM, 2% agar containing 100]lg/ mL, 500]lg/ mL or 1mg/ mL G418; or 50]lg/ mL Hygromycin B) and incubated at 23°C for 7-14 days. Individual colonies obtained on plates were cultured in liquid medium and screened appropriately. Limiting dilution was used to isolate single clones.

Preparation of Leishmania culture for electroporation: An early log phase culture of Leishmania donovani was harvested and dead cells pelleted at 129

Foreign DNA can be introduced into Leishmania cultures using electroporation. Transfected circular plasmids are maintained as episomes, while linear DNA can integrate into the genome. Preparation of DNA : DNA construct to be electroporated was generated using standard molecular biological techniques as described later. The plasmid DNA was prepared from E. coli DH5-a or XL-1 Blue cells using the EndoFree MaxiPrep kit from Qiagen (Hilden, Germany) according to manufacturer's protocol. Briefly, 200mL of overnight culture was pelleted at 6000 x gat 4°C for 15 min. The pellet was resuspended in 10mL Buffer P1 (50mM Tris-Cl, pH 8.0, 10mM EDTA, 100p.g/mL RNaseA). To this 10mL Buffer P2 (200mM NaOH, 1 %w /v SDS) was added and mixed thoroughly by vigorously inverting 4-6 times and an incubated at RT for 5 mins. Now 10mL of chilled Buffer 3 (3.0M Potassium acetate, pH 5.5) was added and mixed thoroughly by vigorously inverting 4-6 times and then the lysate was poured into a QIAfilter catridge and incubated at RT for 10 min. Subsequently a plunger was used to filter the cell lysate into a 50mL tube to which 2.5mL Buffer ER was added and inverted 10 times to mix. This was incubated on ice for 30 min. In the meantime, a QIAGEN-tip was equilibrated with 10mL Buffer QBT (750mM NaCl, 50mM MOPS, pH 7.0, 15%v /v isopropanol and 0.15%v jv Triton X-100). After incubation, the filtrate was allowed to enter the tip resin by gravity. This was followed by two washes with 30mL of Buffer QC (1.0M Nacl, 50mM Tris-Cl, and pH 7.0 and 15% v /v Isopropanol). DNA was eluted with 15mL Buffer QN (1.6M NaCl, 50mM MOPS, pH 7.0 and 15%v /v isopropanol) and precipitated by adding 10.5 mL (0.7 volumes) isopropanol at RT and centrifugation at 15,000 x g for 30 min at 4°C. The pellet was washed with 5mL endotoxin-free 70% ethanol at RT and centrifuged at 15000 x g for 10 min. The pellet obtained was air dried for 5-10 min and redissolved in a suitable volume of endotoxin-free buffer TE (10mM Tris-Cl, pH 8.0, 1mM EDTA). The concentration of the obtained DNA was estimated by measuring the absorbance at 260nm (A260) and using the known formula: DNA concentration = A260 X SOX dilution factor.

Transfection of Leishmania donovani promastigotes

Primer extension analysis to map thetranscription start site was carried out as describedby Conway et al. (1987) and Rajkumari et al. (1997). 20 pmolof primer was labelled at its 5′-end with 32P-γ-ATP as described above. 106cpm equivalent of labelled primer was mixed with 10μg of total cellular RNA. Sodium acetate pH-5.5 was added to a final concentration of0.3 M and the nucleic acids were precipitated with ethanol, washed with 70% alcohol,air-dried and dissolved in hybridization buffer (9 mM Tris-Cl, pH-8 and 0.35 mMEDTA) and incubated overnight at 43ºC for annealing. Reverse transcriptase reactionwas performed by the addition of 5 mM MgCl2, 1 mMdNTP’s, 1 X RT buffer, highconcentration (10 units) of Superscript III Reverse Transcriptase (Invitrogen) to the mixture of annealedlabelled primer and RNA. The reaction was incubated at 43ºC for 1-hr following whichthe nucleic acids were precipitated with absolute alcohol and 0.3 M CH3COONa, pH-5.5. The precipitate was air dried and dissolved in water and gel-loading dye (95%formamide, 20 mM EDTA, 0.05% each of xylene cyanol and bromophenol blue) wasadded. The samples were heated at 90ºC for 2-min before loading on a 6% denaturingpolyacrylamide gel for electrophoreticresolution alongside a sequencingladder

Primer extension analysis

PCR products were purified using the PCR Purification Kit (Qiagen) as per the manufacturer's instructions

Purification of PCR products

A differential gene expression microarray with respect to argP was performed by Genotypic Technology Pvt.Ltd., Bengaluru. The experiment was performed on an oligonucleotide microarray having 10828 probes for coding region(on average three probes were designed for each 4294 coding regions) and 4380 probes for non-coding region (on average two probes were designed for 2240 non-coding regions). The RNA was labelled using Cy3 and single channel detection was used. Data was analysed using GeneSpring GX Version 7.3

Microarray details

Antibiotics were used at the following final concentrations in various media as given inTable 2.4.Table 2.4Concentrations of antibiotics (μg/ml)

Antibiotics

Intracellular reactive oxygen species (ROS)levels in yeast cells weredetermined usingfluorescent probe 2',7'-dichlorofluorescein diacetate (DCFH-DA; Sigma# D6883). Cellular esterasesremove the diacetate groups ofthe DCFH-DAand produceDCFHwhich getsreadily oxidized to highly fluorescent product 2′,7′-dichlorofluorescein (DCF) by intracellular ROS. The fluorescent intensity of DCF corresponds to the amount ofintracellular ROSpresent in the cell.Cells grown under different environmental conditions were harvested,washed once with tissue-culture grade phosphate-buffered saline (PBS) and resuspendedin PBS to the final cell density of 1 OD. Freshly-prepared DCFH-DA (0.01M stock in DMSO) was added to the cell suspension toafinal concentration of 100 μM. Cell suspension was mixed and incubated at 30 ̊C for 30 min. After incubation,cells were washed 2-3 times with 1 ml PBS and then resuspendedin 200 μlPBS. Fluorescence intensity values wererecorded usingspectrofluorophotometer (Varioskan flash-3001, Thermo Scientific) with excitation and emission at 488and 530 nm,respectively.Fluorescenceintensityvalues obtained from probe-loaded cells were subtracted from the fluorescence intensity values obtainedfrom cells-alone samplesto remove background fluorescence

Determination of intracellular reactive oxygen species (ROS)levels

C. glabrataTn7insertion mutantlibrary was screened for reduced growth in YNB-pH 2.0 medium. Thismutant library,composed of 9,134 Tn7insertion mutants, isarrayed in 96-well microtitre plates(Castaño et al.,2003). 2 μlof each mutant strain was inoculated in 120μl YNB medium and grown overnight at 30 ̊C in an incubator with constant shakingat 120 rpm. Overnight grown cultures were 120-folddiluted with 1X PBS in a 96 well block and transferred, using a 96-well pin replicator, to YNB and YNB-pH 2.0 medium. Plates were incubated at 30°C and mutant phenotypes were recorded after 3-4days.

Screening of C. glabrataTn7insertion mutants

suspension was kept on ice for 10 min and 50 μl volume was aliquoted to chilled sterile microcentrifuge tubes. Cellswere immediately snap-frozen in liquid nitrogen and stored at -80 ̊C

A single colony of E.coli DH5-α strain was inoculated in 10ml LB medium and incubated at37 ̊C for overnight. 4 ml of thisovernight culture was inoculated in 2 lt SOB medium and incubated at 18 ̊C till theOD600reaches to 0.5. Cells were harvested by centrifugation at 2,500 g for 10 min at 4 ̊C and washed gently in 80 ml ice-cold Inoue transformation buffer. Cells were collectedby centrifugation at 2,500 g for 10 min at 4 ̊C and gently resuspended in 20 mlice-cold Inoue transformation buffer. To this cell suspension, 1.5 ml sterile DMSO was added and swirled gently. Cell

E. coli DH5α ultra-competent cells preparation

Colony blot assay was performed to analyse secretion of carboxypeptidase Y(CPY)as described previously (Roberts et al., 1991). Single colony of a C. glabratastrain was inoculated in YPD medium andculture was grown till stationary phase. 0.1 OD600equivalent cellsfrom this culture were spotted on CAA medium,overlaidwith a nitrocellulose membrane and plate was incubated at30 ̊C for 18-20 h.Afterincubation, nitrocellulose membranewas washed with water to remove cells and membrane-bound CPYwas detected by immunoblotting with polyclonal anti-CPY antibody at a dilution of 1:10,000

Colonyblot assay

Stripping of membranes in buffer containing 0.4 M NaCl yielded slightly better results. Hybond membranes were reused for 5-10 times after stripping

Radiolabeled-bound probes were stripped from the membrane by boiling in 1% SDS containing 0.1X SSC for 15 min. Alternatively, membraneswereincubatedtwicein stripping solution (0.4 M NaOH)at 45°C for 30 minto remove the bound probes

Stripping of probes from hybridized membranes

24 h post infection, THP-1 macrophages were washed thrice with PBS, lysed in water and recovered yeast cells were used to infect THP-1 cells at a MOIof 1:10. Three rounds of macrophage infection foreach mutant pool were carried out to enrich for the desired mutants in the final population. The lysate of 3rdround infection was inoculated in YPD medium for overnight (output). Cells were harvested, genomic DNA isolated from each input and output cell pellet andunique signature tags were PCR-amplified with P32-labeledα-dCTP using primers complementary to theinvariant region flanking each unique tag sequence. LabeledPCR products were denatured at 95°C for 10 min, chilled on ice and were hybridized tonylon membranescarrying immobilized plasmid DNA containing 96 unique tagsfor 14-16 h at 42°C.Membranes were washed twicewith 0.1X SSC bufferand exposed to phosphorimager screen for 2-4 h. Radioactive counts for each spot were quantified using Image Quant and Fuji Multi Gauge V3.0 software. Relative percentage intensity for individual spot was calculated with respect to allspots present oneach hybridizedmembrane

YPD-grown cultures (0.05 OD600) of each mutant pool (96 mutants, each carrying a unique signature tag) were either inoculated in YPD medium for overnight (input) or used to infect differentiated THP-1 cells (1X106). After 2 h incubation, non-cell-associated yeastcellswere removed by washing THP-1 cellsthricewith PBS. At

Screening of C. glabrataTn7insertion mutant library

THP-1 cells were seeded ina 24-well tissue culture plate to a celldensity of 1 million cells per well,treated with PMA and were infected with yeast cells to a MOIof 10:1. Two hours post infection, cells were washed thrice with PBS and medium was replacedwith fresh prewarmed RPMI medium.Plates wereincubatedat 37ºCfor 24 h. Supernatants were collected,centrifuged at 3,000 rpm for 5 minto get rid of particulate matter,if any, andwerestored at -20°C until use. Estimation of different cytokines wasperformed using BD OptEA ELISA kits as per the supplier’s instructions

Cytokines measurement

Spheroplast resuspension buffer0.1M KCl15 mM HEPES (pH 7.5)3 mM Ethylene glycol-bis(2-aminoethylether)-N,N,N′,N′-tetraacetic acid(EGTA)10% GlycerolPhosphatidylinositol sonication buffer10 mM HEPES (pH 7.5)1 mM EGTA PI3-kinase reaction buffer40 mM HEPES (pH 7.5)20 mM MgCl280 μM ATP5 μCi γ-P32ATPDeveloping solution for thin layer chromatography(120.2 ml)Chloroform –60 mlMethanol –47 mlAmmonia –4.4 mlWater –8.8 ml

Reagents for PI3-kinase assay

SDS-loading buffer was prepared as a 4X stock solutionin H2Oand used at a 1X concentration.SDS-PAGE running buffer0.25 M Tris-HCl (pH 8.0)1.92 M Glycine1% SDSRunning buffer was preparedas a 10X stock solution and diluted to 1X concentration before use.Buffers for Western blotanalysisTransfer buffer (10X stock solution)0.25 M Tris-HCl (pH 8.0)1.92 M Glycine1% SDSTransfer buffer was prepared as a 10X stock solution and diluted to 1X concentration.1X Transfer buffer (1 litre)200 ml of methanol100 ml of 10X transfer buffer700 ml of waterTris-BufferSaline (TBS)25 mM Tris150 mM NaClpH was adjusted to 7.4 with HCl.TBS buffer was prepared asa10X stock solution and diluted to 1X concentration.Blocking and wash buffers (PBS-T and TBS-T)5% Fat-free milk0.1% Tween-20Volume was made to 100 ml with 1X TBS

1 mM sodium orthovanadate1 X protease inhibitor cocktail SDS-PAGE30% Acrylamide solution29 g Acrylamide1 gBis-acrylamideDissolved in 100 ml H2O.10% Sodium Dodecyl Sulfate (SDS)10 g SDS in 100 ml H2OResolving gel mix (12%) (20 ml)6.6 ml H2O8 ml 30% acrylamide:bisacrylamide (29:1) mix5 ml 1.5 M Tris-HCl (pH 8.8)200 μl 10% SDS200 μl 10% Ammonium persulfate(APS)8 μl N,N,N′,N′-Tetramethylethylenediamine(TEMED)Stacking gel mix (5%, 6 ml)4.1 ml H2O1 ml 30% acrylamide:bisacrylamide (29:1) mix750 μl 1 M Tris-HCl (pH 6.8)60 μl 10% SDS60 μl 10% APS6 μl TEMEDSDS loading buffer130 mM Tris-HCl (pH 8.0)20% (v/v) Glycerol4.6% (w/v) SDS0.02% Bromophenol Blue2% DTT

Whole cell lysis buffer (Homogenizing buffer)50 mM Tris-HCl (pH 7.5)2 mM EDTA10 mM sodium fluoride

Buffers for protein extraction and analysis by SDS-PAGE (sodium dodecyl sulphate-polyacrylamide gel electrophoresis)

150 mM NaCl1% Triton-X1% SDSBuffer B50 mM Tris-HCl (pH 7.5)10 mM EDTA1.1 MSorbitol50 mM β-mercaptoethanol (To be added just before use)Buffer C100 mM Tris-HCl (pH 7.5)10 mM EDTA10% SDSAE buffer3 M Sodium acetate(pH 5.3)0.5 M EDTA (pH 8.0)Phenol:Chloroform:Isoamyl alcohol (25:24:1) solution25 ml Tris-equilibrated Phenol24 ml Chloroform1 ml Isoamyl alcholDNA sample loading buffer0.25% Bromophenol blue0.25% Xylene cyanol15% FicollDNA sample loading buffer was prepared in water

Buffer A50 mM Tris-HCl(pH 8)10 mM EDTA

Buffers for extraction and analysis of genomic DNA and RNA

Stripping solutionfor DNA1% SDS0.1% SSCDesired volume was adjusted with sterile water. Alternatively, 0.4 M NaOH was also used to stripthe bound probes fromnylon membranes.HEPES [4-(2-Hydroxyethyl)piperazine-1-ethanesulfonic acid] buffer1 M HEPESpH was adjusted to 7.5 with NaOH.HEPES was used as a buffering agent for preparing plates of YNB medium of different pH. Buffer was filter-sterilized and stored in an amber-coloured bottle.INOUE transformation buffer10 mM PIPES15 mM CaCl2.2H2O250 mM KCl55 mM MnCl2.4H2OpH was adjusted to 6.7 with 1 N KOH.Yeast transformation reagents1 M Lithium acetate 50% Polyethylene glycol2 mg/ml carrier DNADimethyl sulfoxide (DMSO)Zymolyase cocktail buffer for yeast colony PCR2.5 mg/ml Zymolyase1.2 M SorbitolZymolyase buffer was prepared in 1X PBS

pH was adjusted to 8.5 with glacial acetic acid.TAE buffer was prepared asa50Xstock solution and used at 0.5X concentration.Alkaline denaturing solution for DNAfor membrane preparation0.5 M NaCl0.25 M NaOHVolume was adjusted with sterile water.Denhardt’s solution (50X)1%Ficoll-4001% Polyvinyl pyrollidone1% Bovine serum albuminVolume was adjusted with water and solution was stored at -20°C.Saline Sodium Citrate (SSC) buffer(20X)3.0 M Sodium chloride0.3 M Sodium citrate Volume was adjusted with water and solution was sterilized by autoclaving.Prehybridization Buffer5X SSC5X Denhardt’s solution50% Filtered formamide1% SDSVolume was adjusted with sterile water.Post hybridization wash buffersWash buffer 12X SSC0.1% SDSWash buffer21X SSC0.1% SDS

Phosphate-Buffered Saline (PBS)137 mM NaCl2.7 mM KCl10 mM Na2HPO42 mM KH2PO4pH was adjusted to 7.3 before autoclaving.PBS was prepared as a 10X stock solution and diluted to 1X concentration before autoclaving.Tris-HCl buffer0.5 M Trizma BasepH was adjusted to 7.6 using concentrated HCl.Tris-Cl buffer was prepared as a 10Xstock solution and used at a 1X concentration.Tris-EDTA (TE) buffer10 mM Tris-HCl (pH 8.0)1 mM EDTATris-Acetic acid EDTA (TAE) buffer40 mM Tris base0.5 M EDTA

Common buffers

Buffers and solutions

competent cells pre-inoculum was prepared. A single bacterial colony was picked from LB agar plate that has been incubated for 16-20 hours at 37 °C and inoculated into 3 mlLB medium and incubated overnight at 37 °C temperature with 200 rpm shaking. 1% of this pre-inoculum was sub cultured in 100 ml LB-broth and incubated at 18 °C until OD 600 reached 0.5 -0.6 (approx.). Culture was kept on ice for 10 min. with constant shaking. Cells were pelleted by centrifugation at 2000xg/4°C/8 min. Pellet was resuspended in 40 ml of ice-cold Innoue buffer. Bacterial suspension was kept on ice for 30 min, re-spun at 2000 xg/4°C/8 min. Pellet was resuspended in 8 ml of TB buffer inwhich final concentration of DMSO was 7% and left on ice for 10 min. 100μl aliquots were made and snap frozenin liquid nitrogen and stored at -80 °C

All the salts (10 mM PIPES, 15 mM CaCl2.2H2O, 250 mM KCl,55 mM MnCl2. 2H2O) except MnCl2were dissolved in water and pH was adjusted to 6.7 with 1N KOH. MnCl2was dissolved separately in water. MnCl2was added drop wise while stirring (MnCl2if added directly will give a brown colour to the solution and precipitates;hence it needs to be dissolved separately). Solution was then sterilized by filteringand stored. To prepare

PreparationofUltra competent cells

Equal amount of proteins were loadedon an appropriate percentageof denaturing SDS-PAGE gel. After completion ofthe run, the gel was over laid on a PVDF membranecut to the size of gel and sandwiched between filter paper sheets and kept inthe blotting cassette in the presence of transferbuffer. Finally the cassette was put in themini transblotapparatus and blotting was done for 2-3hours at a constantvoltage of 80Vat 4⁰C. For blocking the nonspecific sitesmembrane was incubated with blocking solution(5% non-fat milk solution in TBST)with gentle shaking for 1 hourat room temperature. Excess milk from the membrane was washedoff with TBST and themembrane was incubatedwith primary antibody diluted in 1XTBST for 3 hours atroom temperature or overnight at 4°C withshaking. After incubation the membrane was washedwith TBST and incubatedwithappropriate secondary antibody (conjugated with horse-radish peroxidase)diluted in5% fat free milk solution (in TBST) for 1hat room temperature.The blotwas later washed thricefor 10min eachwith TBST and processed for the detection of proteinsignal using ECL-prime chemiluminescencedetection reagent followed by detectionof signal either on X-ray filmor in a chemiluminescence detectionsystem(Proteinsimple, California, USA)

Immunoblotting

Binding Buffer (10X)

EMSA Buffer

Nuclear lysis buffer

Polydeoxy (Inosinate-cytidylate) (Poly dI-dC)

For Electrophoretic mobility shift assay (EMSA)

TBST

Dithiothreitol (DTT)ComponentsFinal concentrationFor 5 mlDTT1.0M0.7725gH2Oq.s

Materials and Methods462.2.5 Cell proliferation assayThe method described earlier by Gilliesand co-workerswas slightly modified and followed (Gillies et al.,1986). Briefly, parentaland profilin-stable cells were seeded in triplicates at a density of 20,000 cells per well of a 24-well culture plates. Each day after seeding, cells were washed with PBS and stained with 0.2% crystal violet in 2% ethanol for 15 minutes. Vigorous washing was done with PBS to remove excess dye. Crystal violet dye was then eluted using 1% SDS solution with extensive pipetting and diluted 10 fold. Absorbance of the extracted dye was then determined at 570 nm in a spectrophotometer. Absorbance data based on triplicate set of samples for each experimental condition were then averaged for each time point to generate a growth curve.2.2.6 Preparation of whole cell, cytoplasmic and nuclear lysatesIn order to extract the total cell homogenate, the culture media was removed and cells were washed with ice cold PBS. The cells were then gently scrapped and pelleted by centrifugation at 3000 rpm for 3 minutes at 4°C. The cell extraction buffer was added to the cell pellet and placed on rotor kept in cold room for 30 minutes for cell lysis. Lysed cellswere then centrifuged at 13000 rpm for 10min at 4°C. The supernatant was collected as cellular lysate. Protein concentration was estimated using Bradfordassay, described below.For a typical Western blot assay, 30-70μg of protein was loaded on theSDS-PAGE.For the preparation of cytoplasmic lysate,ice-cold hypotonic cytoplasmic extract buffer was added in the cell pellet andgently mixed with the pipette in a microfuge tube. The cell suspension was incubated on ice for 30 minto allow them to swell.After incubation, freshly prepared 10% NP-40was added andvortexed vigorously for 15 seconds torupture the plasma membrane. The contents were then centrifuged at 13000 rpmfor a minuteat 4°C and supernatant containing the cytoplasmic lysate was transferred to another pre-chilled microfuge tube and stored at –70°C.The pellet was then further processed for extraction of nuclear lysate.For this, ice-cold nuclear extractbuffer was added to the pellet and incubated on ice for 45 min with intermittent vortexingafter every 10 min of incubation. Finally, cell suspension wascentrifuged for 5 min at 14000rpm. The supernatant containing nuclear lysatewas stored at –70°C for further experiment

Preparation of whole cell, cytoplasmic and nuclear lysates

For preparation of Ultra competent cells

Inoue buffer

(f) Running buffer

Yeast weregrown in YPD (Difco) overnight,and sub-cultured at 0.2 OD600. Cells were harvested at 0.6-0.8 OD600. 1 OD600of each culture was used for the labelling. Cells were washed in SC-Metmedium twice, suspended in SC-Metmedium containing 25μCi/mLof 35S Met-Cys and pulsed for 15 min. Cells were washed twice in methionine-free medium and suspended in 300Lof Tris-saline. Cell suspension was counted in a liquid scintillation counter (Perkin Elmer-Tricarb 2900). The cpm values obtained were plotted using GraphPad Prism5

35S-Met uptake assay

0.83mL1.5 M Tris-HCl,pH 6.8 50μL10% SDS 50μL10% Ammonium persulfate (APS)8 μLN,N,N′,N′-Tetramethylethylenediamine (TEMED)Resolving gel mix (12%) (20 ml)6.6 mLH2O 8 mL 30% acrylamide:bisacrylamide (29:1) mix 5 mL1.5 M Tris-HCl,pH 8.8 200 μL10% SDS 200 μL10% Ammonium persulfate (APS)8 μLN,N,N′,N′-Tetramethylethylenediamine (TEMED)

Whole cell lysis buffer for yeast (Homogenizing buffer) 50 mM Tris-HCl,pH 7.52 mM EDTA yeastprotease inhibitor cocktail SDS-PAGE 30% Acrylamide solution 29 g acrylamide 1 g bis-acrylamide dissolved in 100 mLH2O. 10% sodium dodecyl sulfate (SDS) 10 g SDS in 100 mLH2O Stacking gel mix (6%)(5 mL)3.4mLH2O 0.63mL 30% acrylamide:bisacrylamide (29:1) mix

Buffers for SDS-PAGE (sodium dodecyl sulphate-polyacrylamide gel electrophoresis)

20 mM HEPES500 mM NaCl 2 mM EDTA1% Triton-XYeast protease inhibitor cocktail and phosphatase inhibitor cocktail (added fresh to the buffer C)IP7 reaction buffer(10X)250 mM HEPES,pH 7.4500 mM NaCl60 mM MgCl210 mM DTT (1 M stock was made separately, aliquoted into 100 μL and stored at -20oC).10X buffer was made and stored at 4oC. An appropriate amount was added to the reaction mix to get a final concentration of 1X.DTT was added fresh to the reaction buffer just before use

Buffer C

2 mM EDTA5 mM DTT1% Triton-XYeast protease inhibitor cocktail and phosphatase inhibitor cocktail (added fresh to the buffer B)

20 mM HEPES pH 6.8100 mM NaCl

Buffer B

20 mM HEPES pH 6.8100 mM NaCl2 mM EDTA5 mM DTTYeast protease inhibitor cocktail and phosphatase inhibitor cocktail (added fresh to the buffer A)

Buffer A

Buffers for protein purification and IP7reaction

Buffer A1 mM EDTAin HPLC grade water (Fisher Scientific)Buffer B 1 mM EDTA(NH4)2HPO41.3 M, pH 3.8171.6 g of (NH4)2HPO4was dissolved in 750 mL of HPLC grade water. pH was adjusted to 3.8 with 75 mL of H3PO4by continuous stirring and the volume was made upto 1000 mL.Both buffers were filtered througha0.22 μm filter (Millipore) using vacuume filter apparatus (Tarsons) and degassing was performed atleast for 20 min using a vacuume pump

Buffers for IP7 purification

Wash buffer II10 mM Tris-HCI,pH 8.01 mM EDTA250 mM LiCl0.75% NP-400.75% sodium deoxycholateProtease inhibitor cocktailElutionbuffer II50 mM Tris-HCl,pH 8.0 10 mM EDTA 1% SDS

Lysis buffer50 mM HEPES,pH 7.5140 mM NaCl1% Triton X-1000.1 % sodium deoxycholate1 mM EDTAProtease inhibitor cocktail (added fresh)Wash buffer I50 mM HEPES,pH 7.5500 mM NaCl1% Triton X-1000.1 % sodium deoxycholate1 mM EDTAProtease inhibitor cocktail

Buffers for chromatin immunoprecipitation

Volume was adjusted with water to 1 L and solution was sterilized by autoclaving.Pre-hybridization/hybridization buffer (Modified Church and Gilbert buffer)0.5 M phosphate buffer (134g of Na2HPO4.7H2O,4 mL of 85%H3PO4), pH7.27% (w/v) SDS10 mM EDTA Volume was adjusted to 1 L with DEPC treated sterile water. Buffer was aliquoted into 50 mL RNase free conical tubes (Corning) and stored in -20oC.Post hybridization wash buffersWash buffer 1 2X SSC 0.1% SDS Wash buffer 2 1X SSC 0.1% SDSWash buffer 3 0.5X SSC0.1% SDSBuffers were prepared with sterile DEPC treated water

TMN buffer10mM Tris-HCl, pH 7.45 mM MgCl2100 mM NaCl Permeabilization buffer950 μLof coldwater50 μLof 10% (wt/vol)sodium N-lauroyl sarcosineTranscription assay buffer(100 μL)50mM Tris-HCl, pH 7.4100mMKCl5mM MgCl21mM MnCl22 mM dithiothreitol 0.5mM ATP 0.25 mM GTP0.25mM CTP10mM phosphocreatine2.4 units creatine phosphokinase100μCi [α-32P] UTP (3,000Ci/mmol)Alkaline denaturing solution for DNA for membrane preparation0.5 M NaCl 0.25 M NaOH Volume was adjusted to 20 mLwith sterile water. Saline Sodium Citrate (SSC) buffer (20X) 3.0 M Sodium chloride 0.3 M Sodium citrate

Buffers fortranscription run on analysis

50 mM Tris-HCl,pH7.450 mM NH4Cl12 mM MgCl21 mM DTT0.1%DEPC37% sucrose solution

100mM NaCl30mM MgCl250μg/mLcycloheximide 200μg/mL heparin All the components were made in DEPC treated water.Gradient buffer10% sucrose gradient buffer50 mM Tris-HCl,pH7.450 mM NH4Cl12 mM MgCl21 mM DTT0.1%DEPC10% sucrose solutionTo analyse individual ribosome subunits, MgCl2 was eliminated from the gradient buffer.30% sucrose gradient buffer50 mM Tris-HCl,pH7.450 mM NH4Cl12 mM MgCl21 mM DTT0.1%DEPC30% sucrose To analyse individual ribosome subunits, MgCl2 was eliminated from the gradient buffer.50% sucrose gradient buffer50 mM Tris-HCl,pH7.450 mM NH4Cl12 mM MgCl21 mM DTT0.1%DEPC50% sucrose To analyse individual ribosome subunits, MgCl2 was eliminated from the gradient buffer.37% sucrose gradient buffer

Lysis buffer10mM Tris, pH7.4

Buffers for ribosome and polysome analysis

30%GlycerolMade in 100 mL.RNA sample loading buffer (10X)50% glycerol10mM EDTA 0.025% Bromophenol blue 0.025% Xylene cyanolInoue transformation buffer, pH 6.7(125 mL, prepared just before use)10 mM PIPES 15 mM CaCl2.2H2O 250 mM KCl 55 mM MnCl2.4H2O (1.361 g is dissolved in 10 mL of water separately)PIPES(0.307 g), CaCl2.2H2O (0.275 g) and KCl (2.325 g)were added to 80 mL ofsterile water while mixing with a magnetic stirrer and the pH was adjusted to 6.8with 1 N KOH. After attaining the appropriate pH, MnCl2solution wasadded slowly in aliquotes of 300 μL over 10 min,while stirring to avoidabrown precipitate.MOPS buffer(10X)0.2 M MOPS, pH 7.220 mM CH3COONa10 mM EDTABuffer was made in DEPC treated waterYeast transformation reagents1 M Lithium acetate 50% Polyethylene glycol2 mg/mLSalmon sperm carrier DNA Dimethyl sulfoxide (DMSO) Zymolyase cocktail buffer for yeast colony PCR 2.5 mg/mLZymolyase (ZymoResearch)1.2 M SorbitolZymolyase buffer was prepared in 1X PBS

Yeast lysis buffer for genomic DNA extraction50 mM Tris-HCl,pH 8.010 mM EDTA 150 mM NaCl 1% Triton-X 1% SDSAE buffer for RNA extraction50 mMSodium acetate,pH 5.31 mMEDTA,pH 8.0Solution was made in DEPC treated water. 0.2%diethyl pyrocarbonate (DEPC)was added to the water and stirred for 12 h. To remove DEPC,water was autoclaved twice. DNA sample loading buffer (6X)15.25 mg Bromophenol blue15.25 mg Xylene cyanol

Buffers for extraction and analysis of genomic DNA and RNA

EDTA (pH 8.0)186.1 g of EDTA.2H2O was dissolved into 800 mL of water stirredvigorously and the pH was adjusted with NaOH pellets. When the pH of the solution reached8.0 EDTA dissolvedcompletely and was made upto 1000 mL with water.Tris-HCl buffer (1M)121.1 g of Tris base was dissolved in 800 mLof water and pH was adjusted to 7.2 using concentrated HCl Tris-EDTA (TE) buffer 10 mM Tris-HCl, pH 8.01 mM EDTA Tris-Acetic acid EDTA (TAE) buffer 40 mM Tris base 1mMEDTApH was adjusted to 8.4with glacial acetic acid. TAE buffer was prepared as a 50X stock solution and used at 1Xconcentration.Tris-Saline20 mM Tris-HCl, pH 7.20.9% NaCl

PhosphateBuffered Saline (PBS) 137 mM NaCl 2.7 mM KCl 10 mM Na2HPO42 mM KH2PO4pH was adjusted to 7.3 using HCl and NaOH beforeautoclaving. PBS was prepared as a 10X stock solution and diluted to 1X concentration before autoclaving

Common buffers

Buffers and solutions

Plasmids containing the shRNA of interestwere either transfected transiently or were stably transfected. Transient transfection of shRNA was performed using eitherLipofectamine 2000 or PEI (as per the method explained before). Stable integration of shRNA was performed by transfecting shRNA along with retroviral packaging vector PCL-Ampho into BOSC23 packaging cells. The supernatantcontaining the packed viruses (viral medium)was collected at 48 and 72 hours of transfection. The viral mediumwas then added to thetarget cells in the presence of polybrene (8μg/mL). Two days later, cells were cultured in medium containing puromycin for the selection of stable clones.The clones stably expressing the desiredshRNA were identifiedandverified through western blotting and immunostaining using specificantibodies. A similar protocol was used to generate stable cell lines that expressed control shRNA

ShRNA

Cells were plated in a manner that they were 30-50% confluent on the day of transfection.Cells were washed with serum-free medium,and the serum-free medium was added to the cells as per plate size. SiRNA was diluted in the serum-free medium, and oligofectamine was diluted in serum-free media, separately (Table 10). Both the complexes were incubated at room temperature for 5 min. Diluted siRNA wasmixed gently with diluted oligofectamine and incubated at room temperature for 15 min. The final transfection mixture was added dropwise to the cells and mixed properly by gentle rocking. Cells were incubated for 4 hrs.,and the growth medium containing 10% FBS was added to the plates without removing the previous medium. Cells were incubated overnight at 37°C in a CO2 incubator. After overnight incubation, the siRNA transfection was repeated using the same protocol. Cells were harvested after 24-48 hours of second round siRNA transfection. The knockdown was detected bychecking the protein levels throughwestern blotting. (Note: SiRNA transfection is carried out in antibiotic free medium)Table 10: SiRNA transfection methodology

SiRNA

RNA interference

In planta growth assay for different strains of Xanthomonas oryzaepv. oryzicolawas performed by counting CFUs. For getting the CFUs, 1 cm2 leaf area surrounding the site of inoculation was cut and surface sterilized by dipping the leaf in 1% (vol/vol) sodium hypochlorite for 2 min followed by three washes with sterile water. To get the CFUs, sterilized leaves were crushed using mortar and pestle, and diluted appropriately for plating on PSA plate containing suitable antibiotics for differentially marked strains

In plantabacterial growth assay

strain or the ∆rpfFmutantharboring the Wild-typeallele in plasmid (pSC9).Genes that were significantly up regulated by 0.6 or more or down regulated by -0.6 or less fold (log2–fold change) were identified.The microarray data have been deposited in the NCBI Gene Expression Omnibus (GEO) under the GEO series accession number GSE53255

8x15k (AMADID: 25096) custom Agilent platform comprised of coding sequences for the three strains of Xanthomonas-X. oryzaepv. oryzae(KACC10331), X. oryzaepv. oryzicola(BLS256) and X. axonopodispv. citri 306 gathered from National Center for Biotechnology Information (NCBI). A total of 8113 probes were designed wherein 2120 probes corresponding to genes of interest replicated three times on Agilent platform. Feature extraction software GeneSpring GX version 10.5.1 of Agilent and GeneSpring GX percentile shift normalization was used for data analysis. Genes that were significantly up or down regulated by more than 1.5 fold and less than 0.5 fold were identified. Hierarchical clustering was performed for the differentially regulated genes and classified based on functional category. Data are the average of two hybridizations from biological replicates of each sample andraw data sets for this study are available at the Gene Expression Omnibus database (Accession number –GSE217809). Likewise, Microarray analysis for Xanthomonas oryzaepv. oryzicolawas performed by isolating RNA from the strains grown under low-ironcondition. The labeled cRNA samples were hybridized on to a Genotypic Technology Private Limited designed 8x15k (AMADID: 41087) Agilent platform. Data extraction from Images was done using Feature Extraction software v 10.7 of Agilent. Data normalization was done in GeneSpring GX using 75thpercentile shift and normalization to specific samples. Differentially regulated genes were clustered hierarchically to identify significant gene expression patterns.Genes were classified based on functional category. Hierarchical clustering of DSF regulated genes in X. oryzaepv. oryzicola grown under low-iron conditions is based on similar expression profiles in ∆rpfFmutant vs either the Wild-typeBXOR1 strain or ∆rpfF(pSC9). Clustering analysis was performed using GeneSpring GX Software using Average Linkage rule with pearson uncentered distance metric. log2–fold change differences between the ∆rpfFmutant with either the Wild-typeBXOR1

Xanthomonas oryzae pv. oryzae strains grown in PS medium to an OD600of 1, were collected, washed once with 150 mM sodium chloride (NaCl) solution to remove excess EPS. RNA isolation was performed using Trizol method described above. After isopropanol precipitation, RNA was frozen at -80°C. Quality of RNA was examined by determining the RNA integrity number (RIN) before microarray analysis. Microarray experiments were performed at Genotypic Technology Pvt. Ltd., Bangalore.Briefly, a

Microarray analysis

shaking at 200 rpm. 1% of overnight grown culture was inoculated in 100 ml fresh PS medium and grown to obtain log-phase culture. Log phase Xanthomonas culture was kept on ice for 10-15 min, aliquoted in 50 ml pre-chilled centrifuge tubes and centrifuged at 4000-5000 g at 4°C for 10 min. Supernatant was discarded and pellet from each tube was gently resuspended in 10-20 ml sterile chilled water. Next, cells were harvested by centrifugation at 4000 g at 4°C for 10 min and supernatant was discarded. Harvested cells were washed twice and finally resuspended in adequate amount of prechilled sterile water. 100 μl of cell suspension was aliquoted in sterile 1.5 ml microcentrifuge tubes and kept on ice. For transformation, Xanthomonaselectrocompetent cells and appropriate amount of plasmid DNA was mixed, and kept on ice in laminar hood. This mixture was added to 1 mm electroporation cuvettes (Biorad) and tapped gently to allow the cells to settle properly in order to avoid air bubbles. Competent cells were electroporated (1800 V, 25 μF, 200 Ω, 1mm cuvette) followed by immediate addition of fresh PS broth in the cuvette, mixed properly and taken in the microcentrifuge tubes. Microcentrifuge tubes containing transformed cells were incubated at 28°C for 2 hours with continuous shaking for recovery. After recovery, cells were plated on specific medium with appropriate antibiotics and incubated in 28°C plate incubator

For electrocompetent cell preparation, single colony of desired Xanthomonasstrain was inoculated in 5 ml PS medium and grown overnight at 28°C

Xanthomonastransformation

Liquid scintillation cocktail5 g PPO (2,5-diphenyloxazol)0.3 g POPOP (1,4-bis (5 phenyl 1,2-oxazole) Benzene Volume was adjusted to 1L with toluene.MUG (4-methylumbelliferyl β-d-glucuronide)extraction buffer1 mM MUG substrate50 mM Sodium dihydrogen phosphate (pH-7.0)10 mM EDTA0.1% Triton X-1000.1% Sodium lauryl sarcosine10 mM β-MercaptoethanolLactophenol solution (100 g)25 g Lactic acid (20.66 ml)25 g Phenol 50 g Glycerol (39.77 ml)These three components were mixed together and 1 volume of lactophenol was added to 2 volumes of ethanol

CAS solutiona) 0.06 g Chrome Azurol S dye in 50 mlb) Fe (III) solution: 10 ml1 mM FeCl310 mM HClc) 0.072 g HDTMA in 40 mlAll the above three solutions were mixed together and autoclaved prior to use

Other solutions

For estimation of tannase activity the reaction mixture (4 ml) contained 1.0 ml of 1.0% tannic acid (prepared in citrate-phosphate buffer, pH 5.0), 2.0 ml of citrate-phosphate buffer (pH 5.0) and 1.0 ml of appropriately diluted culture supernatant. The reaction mixture was incubated at 40°C for 30 min in a water bath. The reaction was stopped by adding 4.0 ml of 2.0% BSA solution. In the control reaction, BSA was added prior to incubation. Now the tubes were left for 20 min,at room temperature, for precipitating the residual tannins and subsequently centrifuged at 10,000 rpm for 20 min. The end product, gallic acid thus formed was estimated by diluting 20 μl of the supernatant to 10 ml with DDW. Now, the absorbance at 260 nm was read against a blank (DDW) in a UV spectrophotometer (1601, Shimadzu Corporation, Japan). One unit of tannase: One tannase unit is defined as the amount of enzyme that releases 1 μmol of gallic acid from the substrate (tannic acid) per ml per min under standard assay conditions

In this method, tannase activity was estimated through spectrophotometric method by determining the concentration of the end product i.e., gallic acid, by estimating the absorbance at 260 nm. Reagents: •Tannic acid (1.0%): The solution was prepared by dissolving 1.0 g of tannic acid in 100 ml of citrate-phosphate buffer of the desired pH.•Bovine serum albumin (BSA): BSA (2.0%) was prepared in citrate phosphate buffer (pH 5.0)

Estimation of tannase activity (Deschamp et. al., 1983)

Overnight-grown C. glabratacells were freshly inoculated either in YNBmedium or YNBmedium supplemented with BPS (50 μM) or FeCl3(500 μM) and allowed to grow for 4 h at 30°C, 200 rpm. After 4 h growth, cells were spun down at 4,000 rpm for 5 min in a refrigeratedcentrifuge set at 4°C and total protein was isolated. For estimation of histone deacetylase (HDAC) activity, 40 μg of protein samples were taken and HDAC Fluorometric Activity Assay Kit (#10011563; Cayman Chemical Company, Ann Arbor, MI, USA) was used as per manufacturer’s instructions. Fluorescence intensity values obtained inthepresence of the HDAC inhibitor, trichostatin A, were subtracted from those of the samples without inhibitorand plotted as relative arbitrary fluorescence units

Estimation of histone deacetylase (HDAC) activity

Bacterial plasmid DNA was isolatedusing the QIAprep® spin Miniprep kit (QIAGEN, 27106). 10 ml of LB medium supplemented with appropriate antibioticswas inoculated withasingle bacterial colony and incubated at 37°C for 12-16 h. Cultures were spun down at 8,000 rpm for 5 min, supernatant was discarded and the cell pellet was processed to isolate plasmid DNA as per instructions given in the kit. DNA was eluted either in nuclease-free water or in elution buffer provided in the kit and stored at -20°C until use

Plasmid isolation

Bacterial transformation

Bacterial plasmid DNA was isolatedusing the QIAprep® spin Miniprep kit (QIAGEN, 27106). 10 ml of LB medium supplemented with appropriate antibioticswas inoculated withasingle bacterial colony and incubated at 37°C for 12-16 h. Cultures were spun down at 8,000 rpm for 5 min, supernatant was discarded and the cell pellet was processed to isolate plasmid DNA as per instructions given in the kit. DNA was eluted either in nuclease-free water or in elution buffer provided in the kit and stored at -20°C until use

Plasmid isolation

E. coliDH5α ultra-competent cells were used for all bacterial transformations. Briefly, frozen DH5α ultra-competent cells were taken out from -80°C freezerandthawed on ice for 15 min. DNA to be transformed was added to the bacterial cell suspension and incubated on ice for 30 min. For transforming ligation mixtures and plasmids,5-10 μl and 100-500 ng of DNA was used, respectively. Followed by 30 min incubation on ice, heat shock was given for 60-90 sec at 42°C in a water bath and cells were immediately kept back onice for 2 min. To this,1 ml of sterile LB medium was added and tubes were incubated inashaker incubator set at 37°C, 200 rpm for 45 min.Next, cells were spun down and resuspended in 500 μl of LB medium. About 100-200 μl of resuspended cells were plated on LB-agar medium containing appropriate antibiotics and incubated for 12-16 h at 37°C. Transformants were purified on LB-agar plates containing appropriate antibiotics andpositive transformantscarrying desired DNAwere verified by PCR, restriction digestion and sequencing analyses

Bacterial transformation

Stripping buffer100 mM β-mercaptoethanol2 % SDS62.5 mM Tris-HCl (pH 6.7)Final volume was madeto 250 ml with water

Transfer buffer (10 X stock solution)0.25 M Tris-HCl (pH8.0)1.92 M Glycine1% SDSThe stock solution was prepared asa10 X concentrate and was diluted to 1 X concentration prior to use.1X Transfer buffer (1 litre)200 ml Methanol100 ml 10X Transfer buffer700 ml WaterTris-Buffered Saline (TBS)50 mM Tris150 mM NaClFinal pHof the bufferwas adjusted to 7.4 with HCl.Blocking buffer5% Fat-free milk0.1% Tween-20Final volume was made to 100 ml with 1 X TBS.Wash buffer (TBS-T)TBS (1 X final concentration)0.1% Tween-20Final volume was prepared with water

Buffers for western blot experiment

2% DTTThe stock solution of SDS loading buffer was made asa4 X concentrateand was added to the protein sample to the final concentration of 1 X.SDS-PAGE running buffer0.25 M Tris-HCl (pH 8.0)1.92 M Glycine1% SDSThe stock solution was prepared as a 10 X concentrate and was diluted to 1 X concentration prior to use.Resolving gel mix (12%, 10 ml)3.3 ml H2O4 ml 30% Acrylamide:N,N’-Methylenebisacrylamide (29:1) mix2.5 ml 1.5 M Tris-HCl (pH 8.8)100 μl 10% SDS100 μl 10% Ammonium persulfate (APS)4 μl N,N,N′,N′-Tetramethylethylenediamine (TEMED)Stacking gel mix (5%, 3 ml)2.1 ml H2O0.5 ml 30% Acrylamide:N,N’-Methylenebisacrylamide (29:1) mix380 μl 1 M Tris-HCl (pH 6.8)30 μl 10% SDS30 μl 10% APS3 μl TEMED

2% DTTThe stock solution of SDS loading buffer was made asa4 X concentrateand was added to the protein sample to the final concentration of 1 X.SDS-PAGE running buffer0.25 M Tris-HCl (pH 8.0)1.92 M Glycine1% SDSThe stock solution was prepared as a 10 X concentrate and was diluted to 1 X concentration prior to use.Resolving gel mix (12%, 10 ml)3.3 ml H2O4 ml 30% Acrylamide:N,N’-Methylenebisacrylamide (29:1) mix2.5 ml 1.5 M Tris-HCl (pH 8.8)100 μl 10% SDS100 μl 10% Ammonium persulfate (APS)4 μl N,N,N′,N′-Tetramethylethylenediamine (TEMED)Stacking gel mix (5%, 3 ml)2.1 ml H2O0.5 ml 30% Acrylamide:N,N’-Methylenebisacrylamide (29:1) mix380 μl 1 M Tris-HCl (pH 6.8)30 μl 10% SDS30 μl 10% APS3 μl TEMED

Total cell lysis buffer (Homogenization buffer)50 mM Tris-HCl (pH 7.5)2 mM EDTA10 mM Sodium fluoride*1 mM Sodium orthovanadate*1 X protease inhibitor cocktail (Sigma, P 8215)** Were added fresh before use.SDS-PAGE30% acrylamide solution29 g Acrylamide1 g N,N’-MethylenebisacrylamideDissolved in 100 ml H2O10% Sodium Dodecyl Sulfate (SDS)10 g SDS in 100 ml H2OSDS loading buffer130 mM Tris-HCl (pH 8.0)20% (v/v) Glycerol4.6% (w/v) SDS0.02% Bromophenol blue

Buffers for protein extraction and separation by SDS-PAGE (sodium dodecyl sulphate-polyacrylamide gel electrophoresis)

Phenol solution saturated with 0.1 M citrate buffer (pH 4.3 ± 0.2)was procured from Sigma (P4682)

Buffer C100 mM Tris-HCl (pH 7.5)10 mM EDTA10% SDSPhenol:Chloroform:Isoamyl alcohol (25:24:1) solution25 ml Tris-equilibrated phenol (pH 8.0)24 ml Chloroform1 ml Isoamyl alcoholDNA sample loading buffer0.25% Bromophenol blue0.25% Xylene cyanol15% FicollStock solution of the loading buffer was prepared in water as a 6 X concentrate and was added to the sample DNA to the final concentration of 1 X.RNA isolation bufferAE buffer3 M sodium acetate0.5 M EDTA (pH 8.0)Reagents used for RNA isolation were prepared in DEPC-treatedwater and stored at 4°C. For preparationof DEPC-treated water,0.1 ml DEPC was added to 100 ml waterand kept overnight onamagnetic stirrer. Followingincubation,the solution was autoclaved to remove any traces of DEPC.Acid phenol solution

Genomic DNA isolation buffersBuffer A50 mM Tris-HCl10 mM EDTA150 mM NaCl1% Triton-X1% SDSBuffer B50 mM Tris-HCl (pH 7.5)10 mM EDTA1.1 M Sorbitol50 mM β-mercaptoethanol (Added freshbefore use)

Buffers used for nucleicacid extraction

10 mg/ml carrier DNA 5 μlAbove-mentioned reagents were added to prepare thetransformation mixture, and the volumes indicated wereused per transformation.500-1,000 ng of desired transforming DNA was added to this transformation mixture and final volume was adjusted to 360 μl with sterile water.Carrier DNA (Sonicated salmon sperm DNA, Stratagene, 201190) washeat denatured at 95⁰C for 10 min and transferred on ice before additionto the transformation mixture.43 μl DMSO was added to each transformation mixture before heat shock.Zymolyase cocktail buffer for yeast colony PCR2.5 mg/ml zymolyase (MP Biomedicals, 0832092)1.2 M SorbitolThe cocktail was prepared in sterile water

Tris-acetic acid EDTA (TAE) buffer40 mM Tris Base0.5 M EDTAFinal pHof the bufferwas adjusted to 8.5 with glacial acetic acid.TAE buffer was prepared as a 50 Xconcentrate and diluted to 0.5X concentration prior to use as agarose gel electrophoresis running buffer and to cast agarose gels.HEPES [4-(2-Hydroxyethyl)piperazine-1-ethanesulfonic acid] buffer1 M HEPESFinal pHof the bufferwas adjusted to 7.5 with NaOH.HEPES was used as a buffering agent forpreparationof different pHmedium. Buffer was filter-sterilizedby usinga0.22 μm membrane filterand stored at 4°C.INOUE transformation buffer10 mM PIPES15 mM CaCl2.2H2O250 mM KCl55 mM MnCl2.4H2OFor preparation ofINOUE transformationbuffer,above-mentioned solutes were dissolved in appropriate amount in 800 ml of water and then 20 ml of 0.5 M PIPES(piperazine-1,2-bis[2-ethanesulphonic acid])(pH 6.7) was added. Final volume was adjusted to 1 litre with water, buffer was filter sterilized by usinga0.22 μm membrane filter and stored at -20°C. Stock solution of PIPES was preparedseparatelyby dissolving 15.1 gm of PIPES in 80 ml of water, pH was adjusted to 6.7 using 5 M KOH and volume was adjusted to 100 ml.Yeast transformation reagents1 M lithium acetate 36 μl50 % polyethylene glycol 240 μl

Phosphate-Buffered Saline (PBS)137 mM NaCl2.7 mM KCl10 mM Na2HPO42 mM KH2PO4Final pH of the buffer was adjusted to 7.3with 11.6 N HCland volume was adjusted to 1 Lbefore autoclaving.PBS was prepared as a 10X stock solution and diluted to 1 X concentration before autoclaving.Tris-HCl buffer0.5 M Trizma BaseFinal pHof the bufferwas adjusted to 7.6 using 11.6 NHCl.Tris-EDTA (TE) buffer10 mM Tris-HCl (pH 8.0)1 mM EDTATE buffer was prepared as a 10 X concentrate and diluted to 1 X concentration before use

Common buffers