Bacillus subtilis

Engineering the Subtilisin Gene
into E. coli
Oggie Golub
Katy Hood
Derek Stewart
Casy Cory
Josh Mauldin
• Project Goal
– To engineer the aprE gene into E. coli and test for
expression of subtilisin.
• Vector Components
– Antibiotic Resistance Plasmid pSB1A2 (or pSB1A7)
– Arabinose Induced Promoter R0080 (or I0500)
Procedural Overview
BioBrick Library
Bacillus Subtilis
Extraction from
Extraction of
Amplification of
Extraction of
Digestion of Gene
Digestion of
Prepared Plasmid
Prepared Gene
Ligation of Gene
and Plasmid
Transformation into
E. coli
Sequencing and
Testing for Expression
nprE Gene
Cloning Plasmid
• Extracted part pSB1A2+R0080 and pSB2K3+I0500
– Extracted from 2007 & 2008 Library
– Followed Protocols from both Libraries
• Transformed into Competent Cells
– Plated transformants
• pSB1A2+R0080 on Ampicillin
• pSB2K3+I0500 on Kanamycin
– Results
• Only Cells with pSB1A2+R008 from 2007 Showed
• Prepared Glycerol Stocks and Backup Plates
Extracting Plasmid
• Extracted Plasmid from Transformed Colonies
– Followed Protocol from GeneJET Mini Prep Kit
• Ran Digested and Undigested Plasmid on a Gel
– Digested Samples Contained Plasmid and Promoter
Preparing Plasmid for Ligation
• Digested Plasmid
– Used SpeI and PstI Restriction Enzymes
– Followed Protocol from QIAquick PCR Purification Kit
• Ran Digested Plasmid on Gel
– Both the Digested Plasmid and Undigested Plasmid were
Preparing Plasmid for Ligation
• Extracted Digested Plasmid from Gel
– Top Band was Excised from the Gel
– Followed Protocol from QIAquick Gel Extraction Kit
• Ran Gel to Confirm the Plasmid was Ready for
Globiformis and Niger
Glycerol Stock Preparation
• Glycerol Stocks Prepared
– Four overnight cultures were obtained from Dr. Walter
(Niger and Globiformis strains)
• DNA Extraction of B. subtilis
– We used both strains for our extraction
– The procedure we used was found online at OpenWetWare
DNA Extraction Results
Agarose Gel Results
– The results showed no DNA
present and we ran another
gel to double check, which
yielded about the same
– We decided to run a PCR on
the DNA anyways because
there was a possibility that
something might be present
PCR Amplification of aprE
Used a standard PCR setup
Agarose Gel Run of PCR
– The positive control worked
– The DNA did not show up
very bright
– Possible problems:
• Incorrect Primers
• Impure DNA
• DNA Extraction Errors
+ -
Troubleshooting our DNA Extraction
• We wanted to find out if our DNA extraction
procedure works for our DNA samples or if another
procedure would allow us to obtain more purified
• We found a new DNA extraction method online and
obtained new DNA to try out this new procedure
• Extraction protocol found on
Agarose Gel Run of New DNA
The results were unclear for this
particular gel because the gel
had been sitting too long before
we loaded our samples
The result was that everything
was blurry and fuzzy
We believe, however, that some
DNA was present
Optimal Annealing Temperature Test
• Annealing Temperature
– We ran a gradient at five temperatures to find an optimal
annealing point for our future PCR
• 48°, 50.1°, 52°, 54.7°, and 56.8°
– We made five globiformis mixes, five niger mixes, a
positive control, and a negative control for this PCR.
• Agarose Gel Run
– Our results did not turn out
– The Niger samples were
very bright
– Neither the Niger or the
Globiformis samples
appeared to have much
DNA present
DNA Extraction Repeat
Extract New DNA
– We extracted new DNA from
both variations to use when
we’re cloning the aprE gene
– We used the same protocol as
last time
Agarose Gel Run
– We finally had a little success
this time and were able to see
that DNA was present
Annealing Temp Test #2
Ran an annealing gradient for
PCR to find optimal annealing
– We used the same setup and
temperatures as before
– The positive control didn’t
show up.
– Since our controls did not
work, there is no way to tell if
the PCR is running properly.
• Since none of our PCR’s have been successful we
need to come up with backup plans
– We are going to try using a plasmid that was made last
year by a previous group
– We are also going to research obtaining new primers since
we are not having any success with our present ones
Locating Strain 168
• We researched the Bacillus Subtilis Strain 168 online
to try and find somewhere we could purchase it from
• Bacillus Genetic Stock Center
– Ordered original strain from site
Reviving B. subtilis 168
• Revive Bacillus Cultures (Strain 168)
– Arrived in the mail as spore dots on filter disks
– Used the instructions that came with the cultures to revive them
– The bacteria colonies revived well
– We made two liquid cultures and streaked two on LB plates
– Josh and Casy used these cultures to do a DNA extraction and
continue on the Bacillus subtilis route while Derek and I started
a backup plan using Wintergreen
– Oggie worked on cloning the nprE gene
Extraction of Genomic DNA
• Extracted Genomic DNA from B. subtilis 168
– Followed Protocol Found on BioNet
– Digested and Undigested Samples were Run on a Gel
• The Digested Samples were Digested with EcoRI.
Neutral Protease nprE
Neutral Protease (nprE) Project Design
• Aside from subtilisin (aprE) B. subtilis also produces a
neutral protease called bacillolysin
– Coded for by the nprE gene
– Has properties similar to subtilisin
• Alkaline protease vs. neutral protease
• Used NCBI genome database to design forward and
reverse primers
Primer Design
• Three forward and one reverse primer was used to
clone the nprE gene
– F1 designed for entire nprE gene
– F2 designed for just the mature product
– F3 was a mutated version of F2
• Contained less hairpins
– All three contained the same prefix
– Reverse contained the same suffix
Preparing Primers
• Primers came not dissolved
– Dissolved in U.V. treated water to 100 μM
• After dissolving they needed to be dilluted
– 100 μM to 10 μM dillution using U.V. treated water
• Setup a PCR gradient to determine optimal annealing
Annealing Temperature Test Results
Failure again..
– + control worked
– No 1500 bp or 900 bp bands
• “Mystery” band around
200 bp instead
– - controls showed nothing
All results look the same
– Primers self annealing?
– Not according to negative
Testing DNA & R1 Primer
• “Mystery” band of 200 bp showed up only in the
presence of DNA and R1 primer
– Reverse primer acting as forward as well?
– DNA has fragments which act as primers?
• Tested by running PCR with only DNA, and only the
reverse primer
• “Mystery” band showed up
with just DNA
– Band must be part of
genomic DNA
• Reverse primer only showed
– Not acting as forward
Troubleshooting previous aprE failures
• Josh & Casy succeeded in cloning the aprE gene
– Modified primers and used new strain
• Which one resulted in success?
• Performed tests
– Old strains with newly modified primers
– New strain with original primers
• It was necessary to change
both the DNA and primers
– 168 w/ old primers
– G & N w/ new primers
• All look like negative
– - Controls
• Primers only
Positive Control:
Plasmid Test
• Had reoccurring problems with positive controls in our PCR
• Wanted to test two different plasmids as our positive controls
• We used P_Bluescript and BBA_1765001.
• To assess why we were having bad results, we used two other
variables. Temperature (48-56 degrees) and primer dilution
(1/100, 1/10 and 1/1).
Results: We had a misshapen gel, and our results were unreadable. Not shown
are results from another group which confirm the PCR worked.
3/10/2009 (pg.23)
A Shift in gears: Wintergreen
• The part was BBA_1765001, which was already inside
a plasmid.
• Used WGF1 and WRR2 primers.
• Gene of about 1300 b.p. will be cloned from the
construct prepared last semester by “The sweet smell
of, E.Coli?
Initial Amplification
• We were supplied with three samples of plasmid
containing the wintergreen gene (#’s 3,7,8).
• Positive control psB_1A7 (confirmed to work by other
• Three annealing temperatures: 48, 52, 56 degrees.
• PCR program “Onion 1” (See pg.21)
• No bands, shadows may be gen. DNA.
• Positive control and L.R.L in same well.
3/24/2009 (pg.27)
• Same protocol as before.
• Hoping to eliminate and unknown errors in gel
pouring, pipetting, ext.
No banding. However, DNA #3 showed little to no coloration.
Proceeded using DNA #7 and #8 due to activity shown.
Wintergreen Amplification with additional
Attempt to:
Amplify the Wintergreen using both DNA #7 & 8.
Three temperatures as before.
Primer concentrations of 1/1 and 1/10.
Test integrity of plasmid using VF and VR.
• Unfortunately, ran the agarose gel too long, and samples ran into
each other. However, we can see a clear band at the appropriate
size for wintergreen. Also, all VF/VR samples amplified
regardless of temperature.
• The wintergreen
only amplified
at 48 degrees.
The band we see
Had a 1/10 primer
Dilution. DNA #7
3-4-09 (pg.31) Amp of Wintergreen gene @ three temps. @
two primer concentrations, and 2 DNA’s.
Mass wintergreen Production for ligation
• Identical parameters for the band on previous gel in
greater numbers.
• No amplification of the Wintergreen gene.
• Due to some confusion, we had three positive controls, and
three negative controls – all had expected results.
• We conclude we have misinterpreted our results from 3-4-09.
4-9-09 (See Katy Hoods notebook) Wintergreen Amp.
Wintergreen amplification …Thrid times
the charm.
Amplify 10 samples of wintergreen.
Positive & Negative controls.
1/10 DNA dilution.
PCR Protocol “Katy”
• No amplification of wintergreen or positive control.
• Realized we have been using 10X too concentrated
• Redo experiment.
FINAL Wintergreen amp.
Using the proper concentration of primer.
DNA #7
Positive control PSB_1A7 (VF/VR)
• Here we see a faint band around 1.5 k.b. This is in the expected range of
the Wintergreen gene. Our positive and negative controls worked properly.
• You will see two positive controls, one has .8ul VF/VF primer and one has
1.0ul. As you can see, there was no appreciable difference in the two.
4-21-09 (pg. 39) “Mega Final Wintergreen Amp.
Final Thoughts..
• We had several mistakes…
Wrong primer concentration, misinterpreted results,
double well loading, wrong primer, mass confusion.
The wintergreen yielded little to (probably) no actual
gene amplification.
Still loved the class.
Ligations, Transformations, and Results
Initial Primer Problems and Redesign
• The proposed primer sequences were run through the
IDT website. The following hairpins formed.
Forward Primer
Reverse Primer
Amplification of the aprE Gene
• PCR Setup
– Temperatures of 45°C, 50 °C, 55 °C, and 60 °C
– Template Volumes of 0.1 µL and 1 µL
• Ran Gel of PCR Products
– Verified aprE Gene was Amplified
Preparing aprE Gene for Ligation
• Repeated PCR
• Digested aprE Gene
– Used XbaI and PstI Restriction Enzymes
• Ran Gel of Digested Gene
– Top Band was Excised and Extracted
Preparing aprE Gene for Ligation
• Ran Gel to Estimate Gene Concentration
– Concentrated and Dilute Samples were Loaded
– Concentration Calculated to be 13.3 ng/µL
40 ng/10 µL (determine by ladder) = 13.3 ng/µL
3 µL (volume of DNA loaded)
Ligation of the Gene and Plasmid
• The Digested Gene and Plasmid were used for the
Following Ligations
Molar Ratio (Plasmid:Gene)
8.0 µL
4.0 µL
4.0 µL
4.0 µL
0.1 µL
0.1 µL
0.5 µL
0.5 µL
10× Buffer
1.0 µL
1.0 µL
1.0 µL
1.0 µL
1.0 µL
DNA Ligase
1.0 µL
1.0 µL
1.0 µL
1.0 µL
1.0 µL
4.0 µL
3.5 µL
7.5 µL
4.0 µL
Cloning Ligated Plasmid
• Transformed Ligation Products into Competent Cells
– Selected for Ampicillin Resistance
– Results
• Majority of Colonies Resulted from the Ligation with
the 1:1 Molar Ratio
• Ligation Appeared Successful
Extracting Ligated Plasmid
• Extracted Plasmid from Transformed Colonies
– Followed Protocol from GeneJET Mini Prep Kit
– Sequenced Samples
• Ran Digested Samples on a Gel
– Digested with XbaI and SpeI
– Expected Two Fragments
• Promoter–Gene at 1300 bp
• Plasmid at 2000 bp
Project Results
• The aprE gene was not present the colonies obtained.
• Sequencing revealed the plasmid as expected, as well
as the promoter flanked by the appropriate BioBrick
prefix and suffix.
• Possible explanations:
– Gene and Plasmid did not properly ligate.
– Transformation was inefficient.
– Promoter was constitutive resulting in immediate cell