Xylanase Protocols

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==Introduction==
==Introduction==
These protocols are used to screen for and measure xylanase activity.
These protocols are used to screen for and measure xylanase activity.
 +
==Congo Red Staining==
 +
Congo Red is a dye that will bind to carbohydrate polymers (e.g. cellulose and xylan).
 +
===Materials===
 +
*Agar medium of your choice
 +
*Congo-Red solution (1mg/ml in H<sub>2</sub>O)
 +
*Xylan (or carboxy-methyl-cellulose (CMC))
 +
===Procedure===
 +
#Make agar plates containing 0.01% xylan
 +
#Apply a droplet of overnight culture (or you can streak for colonies)
 +
#Incubate for 16 hours.
 +
#Add 10 ml of Congo-Red solution to the top of the plate
 +
#Incubate for 15 minutes to stain xylan.
 +
#Pour off congo-red.
 +
#Observe clearing zones around xylanase positive colonies.
 +
===Notes===
 +
===References===
==Plate Screen==
==Plate Screen==
This is a quick procedure to screen for xylanase activity.
This is a quick procedure to screen for xylanase activity.
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===Materials===
===Materials===
*2.5g Xylan
*2.5g Xylan
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*1L Wash solution (660ml Ethanol, 330ml Water, 1.35g Sodium Acetate)  
*1L Wash solution (660ml Ethanol, 330ml Water, 1.35g Sodium Acetate)  
*Acetone
*Acetone
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===Preparing the Dyed Xylan===
===Preparing the Dyed Xylan===
#Add 2.5g  RBB dye and 2.5g Xylan to 60 ml Water.
#Add 2.5g  RBB dye and 2.5g Xylan to 60 ml Water.
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#Wash the precipitate with 50ml Acetone.
#Wash the precipitate with 50ml Acetone.
#Dry at room temp overnight.
#Dry at room temp overnight.
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===Procedure===
===Procedure===
#Add 0.2% RBB-Xylan (weight per volume) to your agar media of choice and autoclave.
#Add 0.2% RBB-Xylan (weight per volume) to your agar media of choice and autoclave.
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This assay measures the release of reducing sugars (including xylose and arabinose) during the enzymatic treatment of xylan.  If you have reducing sugars (e.g. glucose) in your media, it will also be detected, so you will always have to compare to a control culture with no xylanase.
This assay measures the release of reducing sugars (including xylose and arabinose) during the enzymatic treatment of xylan.  If you have reducing sugars (e.g. glucose) in your media, it will also be detected, so you will always have to compare to a control culture with no xylanase.
===Materials===
===Materials===
-
 
*Copper Sulfate (pentahydrate)
*Copper Sulfate (pentahydrate)
*Ammonium Molybdate (tetrahydrate)
*Ammonium Molybdate (tetrahydrate)
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*Xylan (purified)
*Xylan (purified)
*Xylose (purified anhydrous)
*Xylose (purified anhydrous)
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===Preparing the Reagents===
===Preparing the Reagents===
If you prepare the amounts listed you will be able to run 10 samples (not including the standard curve)
If you prepare the amounts listed you will be able to run 10 samples (not including the standard curve)
====Standard solution====
====Standard solution====
:*This solution is 1mg/ml xylose and you will need 250μL of it.
:*This solution is 1mg/ml xylose and you will need 250μL of it.
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====Substrate Solution====
====Substrate Solution====
:1. Dissolve the following in 10ml of water:
:1. Dissolve the following in 10ml of water:
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:2. Bring the volume up to 20ml by adding water.
:2. Bring the volume up to 20ml by adding water.
:3. Adjust the pH to 4.5 using HCl.
:3. Adjust the pH to 4.5 using HCl.
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====Copper Solution====
====Copper Solution====
:1. Dissolve the following in 10ml of water:
:1. Dissolve the following in 10ml of water:
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::*3.7g Sodium Sulfate
::*3.7g Sodium Sulfate
:2. Bring the volume up to 20ml by adding water.
:2. Bring the volume up to 20ml by adding water.
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====Acid Solution====
====Acid Solution====
:1. Dissolve the following in 10ml of water:
:1. Dissolve the following in 10ml of water:
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::*1.26ml 72% Sulfuric Acid (12M Sulfuric Acid)
::*1.26ml 72% Sulfuric Acid (12M Sulfuric Acid)
:2. Bring the volume up to 20ml by adding water.
:2. Bring the volume up to 20ml by adding water.
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===Procedure===
===Procedure===
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====Standard Curve====
====Standard Curve====
: Prepare the following samples:
: Prepare the following samples:
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::Standard 3 : 70ul of xylose standard and 1.83ml of water and 100 ul of MRS
::Standard 3 : 70ul of xylose standard and 1.83ml of water and 100 ul of MRS
::Standard 4 : 100ul of xylose standard and 1.80ml of water and 100 ul of MRS
::Standard 4 : 100ul of xylose standard and 1.80ml of water and 100 ul of MRS
-
 
====Samples====
====Samples====
:Add 100ul of cell culture (in MRS) to 1.9ml of xylan substrate.
:Add 100ul of cell culture (in MRS) to 1.9ml of xylan substrate.

Revision as of 23:43, 10 October 2011

Contents

Introduction

These protocols are used to screen for and measure xylanase activity.

Congo Red Staining

Congo Red is a dye that will bind to carbohydrate polymers (e.g. cellulose and xylan).

Materials

  • Agar medium of your choice
  • Congo-Red solution (1mg/ml in H2O)
  • Xylan (or carboxy-methyl-cellulose (CMC))

Procedure

  1. Make agar plates containing 0.01% xylan
  2. Apply a droplet of overnight culture (or you can streak for colonies)
  3. Incubate for 16 hours.
  4. Add 10 ml of Congo-Red solution to the top of the plate
  5. Incubate for 15 minutes to stain xylan.
  6. Pour off congo-red.
  7. Observe clearing zones around xylanase positive colonies.

Notes

References

Plate Screen

This is a quick procedure to screen for xylanase activity.

Materials

  • 2.5g Xylan
  • 2.5g RBB (Remazol Brilliant Blue)
  • 60ml Water
  • 20ml Sodium Hydroxide Solution (1.5g in 20ml)
  • 20ml Sodium Acetate Solution (0.675g in 20ml)
  • 200ml 96% Ethanol
  • 1L Wash solution (660ml Ethanol, 330ml Water, 1.35g Sodium Acetate)
  • Acetone

Preparing the Dyed Xylan

  1. Add 2.5g RBB dye and 2.5g Xylan to 60 ml Water.
  2. Add 20ml Sodium Acetate solution to RBB-Xylan solution.
    1. Add dropwise over 5 minutes while stirring at room temp.
  3. After mixing add 20ml Sodium Hydroxide solution.
  4. Stir for 90 minutes at room temperature.
  5. Add two volumes of 96% Ethanol to precipitate the xylan-RBB.
  6. Filter using a vacuum flask and watman filter paper.
  7. Wash the precipitate sequentially with 1L of wash solution.
    1. The filtrate should now be colorless.
  8. Wash the precipitate with 100ml 75% Ethanol.
  9. Wash the precipitate with 50ml Acetone.
  10. Dry at room temp overnight.

Procedure

  1. Add 0.2% RBB-Xylan (weight per volume) to your agar media of choice and autoclave.
  2. Pour the plates immediately being sure to swirl frequently.
  3. Allow to solidify.
  4. Drop 5μL of overnight culture onto the plates (This will look like a large round colony).
  5. Incubate for two days.
  6. Observe clearing zones around xylanase producing cultures.

RBB Assay

This assay functions on the release of ethanol soluble RBB when the RBB-Xylan is cleaved by xylanase. To be sure that there is activity it can be useful to do duplicate samples and measure after 1 hour and then again after 2 hours.

Materials

  • RBB-Xylan (made according to the procedure outlines above)
  • Cell culture (containing the xylanase)
  • water

Procedure

  1. Prepare a 0.1M Acetate buffer containing 11.5mg/ml RBB-xylan
  2. Add 250ml of RBB-xylan solution to 250ml cell culture
  3. Incubate for 2 hours at 30°C
  4. Add 1ml Ethanol to stop the reaction and precipitate RBB-Xylan
  5. Centrifuge for one minute at maximum speed
  6. Collect supernatant
  7. Measure absorbance at 595nM
  • Compare to medium with a no xylanase control
  • Higher absorbance means more xylanase activity

Somogyi Nelson Assay

This assay measures the release of reducing sugars (including xylose and arabinose) during the enzymatic treatment of xylan. If you have reducing sugars (e.g. glucose) in your media, it will also be detected, so you will always have to compare to a control culture with no xylanase.

Materials

  • Copper Sulfate (pentahydrate)
  • Ammonium Molybdate (tetrahydrate)
  • Sodium Acetate (anhydrous)
  • Sodium Bicarbonate (anhydrous)
  • Sodium Carbonate (anhydrous)
  • Potassium Sodium Tartrate (heptahydrate)
  • Sodium Sulfate (anhydrous)
  • Sodium Arsenate (dibasic heptahydrate)
  • Sulfuric Acid (72%)
  • Xylan (purified)
  • Xylose (purified anhydrous)

Preparing the Reagents

If you prepare the amounts listed you will be able to run 10 samples (not including the standard curve)

Standard solution

  • This solution is 1mg/ml xylose and you will need 250μL of it.

Substrate Solution

1. Dissolve the following in 10ml of water:
  • 82mg Sodium Acetate
  • 0.2g Xylan
2. Bring the volume up to 20ml by adding water.
3. Adjust the pH to 4.5 using HCl.

Copper Solution

1. Dissolve the following in 10ml of water:
  • 80mg Copper Sulfate
  • 0.32g Sodium Bicarbonate
  • 0.48g Sodium Carbonate
  • 0.25g Sodium Potassium Tartrate
  • 3.7g Sodium Sulfate
2. Bring the volume up to 20ml by adding water.

Acid Solution

1. Dissolve the following in 10ml of water:
  • 54mg Arsenic Acid
  • 0.13g Molybdic Acid
  • 1.26ml 72% Sulfuric Acid (12M Sulfuric Acid)
2. Bring the volume up to 20ml by adding water.

Procedure

Standard Curve

Prepare the following samples:
Blank sample : 1.90 ml of xylan substrate
Standard 1 : 20ul of xylose standard and 1.88ml of water and 100ul of MRS
Standard 2 : 50ul of xylose standard and 1.85ml of water and 100 ul of MRS
Standard 3 : 70ul of xylose standard and 1.83ml of water and 100 ul of MRS
Standard 4 : 100ul of xylose standard and 1.80ml of water and 100 ul of MRS

Samples

Add 100ul of cell culture (in MRS) to 1.9ml of xylan substrate.
1. Swirl sample, standards, and blank, and bring to 30°C.
2. Add 100ul of water to the blank sample, swirl, and incubate for 10 minutes at 30°C.
3. Add 2ml of copper solution to each standard and blank sample and swirl each solution.
4. Place a marble over each tube and place each tube in a boiling water bath for 10 minutes.
5. Allow tubes to cool to room temperature.
6. Add 2ml of acid solution to each tube and vortex until all precipitate is dissolved and foaming has stopped. Centrifuge tubes.
7. Transfer solutions to cuvettes and measure the absorbance at 540nm.
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