Difference between revisions of "Team:UofGuelph/Description"

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<h1 class="descHead">Project Design</h1>
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<h1 class="descHead">Project Description</h1>
 
<img src="https://static.igem.org/mediawiki/2017/4/4a/T--
 
<img src="https://static.igem.org/mediawiki/2017/4/4a/T--
  
 
U_of_Guelph--gryphon.jpg" class="guelphImages">
 
U_of_Guelph--gryphon.jpg" class="guelphImages">
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<h1 class="descSub">Whats the Deal with Beerstone?</h1>
 
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<p class="descP">
 
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Beerstone can form on any surface that comes into contact
 
  
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with beer and wort (unfermented beer) and has been a
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<h1 class="descSub">Background on Beerstone, FRC and  
  
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problem for brewers as long as beer has been
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OXC</h1>
 +
<p class="descP">
 +
Beerstone is a salt precipitate composed primarily of
  
−
produced<sup>1, 2</sup>. The most problematic locations
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calcium oxalate (C<sub>2</sub>CaO<sub>4</sub>). It poses
  
−
for its formation are heat exchangers, fermentation
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a large problem in the brewing industry due to its high
  
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vessels, aging tanks, kegs, and beer dispense lines. 
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insolubility and use of corrosive chemicals for its
  
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Beerstone is comprised of a combination of precipitated
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effective removal from brewing equipment<sup>1</sup>.
 +
<br><br>
 +
The reason for the high insolubility of beerstone is  
  
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calcium oxalate and entrapped beer
+
because one of its major components, calcium oxalate  
  
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polypeptides<sup>3</sup>. Oxalate enters the brewing
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(C<sub>2</sub>CaO<sub>4</sub>), contains a chelator.  
  
−
process from the cereal grains and hops used to make
+
Calcium ions in the water react with oxalic acids present
  
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beer<sup>4</sup>. Oxalate is present in the form of
+
in malt, forming calcium oxalate. When polypeptides found
  
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aqueous oxalic acid which is a corrosive, highly oxidized
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in beer are incorporated into the oxalate structure, the
  
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compound that has strong chelating activity<sup>5</sup>.
+
precipitate that is formed is known as
  
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These oxalate ions are soluble in both wort and beer,  
+
beerstone<sup>2,3</sup>. Geographic regions that contain
  
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allowing them to combine with calcium ions to form
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high levels of calcium in their drinking water, such as
  
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calcium oxalate<sup>4</sup>. Calcium ions enter the
+
Guelph, Ontario, Canada, can lead to 165g of
  
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brewing process through the water, grains and water-
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C<sub>2</sub>CaO<sub>4</sub> buildup per 1000L batch of
  
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correction salts<sup>4</sup>. Calcium oxalate
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beer<sup>4</sup>.  
 +
The porous nature of beerstone scale promotes biofilm
  
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precipitates out of solution upon formation, and is one
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formation from the microorganisms present in the brewing
  
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of the most insoluble metallo-organic compounds with a
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solution. Biofilm growth causes both “off flavours” that
  
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low solubility<sup>4</sup>. In a geographic region with
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can ruin an entire batch of beer and also be a potential
  
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high calcium levels in the drinking water, such as
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biosafety hazard for the consumer<sup>5</sup>.
 +
<br><br>
 +
<i>Oxalobacter formigenes</i> is a human gut bacterium
  
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Guelph, Ontario, this can lead to up to 165g of calcium
+
that derives its energy solely from the metabolization of  
  
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oxalate building up in a single 1000L batch of
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oxalate using enzymes Formyl-Coenzyme A Transferase (FRC)
  
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beer<sup>1</sup>. This precipitation can happen either
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and Oxalyl-Coenzyme A Decarboxylase (OXC). Oxalate is
  
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during the brewing or bottling processes, or after the  
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brought into the cell by an oxalate-formate antiporter
  
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beer has been bottled depending on when the calcium
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(OxIT) and converted to CO2 and formyl-CoA. The formyl-
  
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oxalate formation occurs<sup>4</sup>. The point during
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CoA is reused by FRC as a CoA donor in a subsequent
  
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the process at which calcium oxalate forms is dependent
+
reaction and released from the cell as formate by
  
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on temperature, time, pH and ion
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OxIT<sup>6</sup>.
 +
</p>
  
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concentration<sup>4</sup>. If calcium oxalate forms after
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<h1 class="descSub">Objectives</h1>
−
 
+
<p class="descP">
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filtration, or if all calcium oxalate crystals are not
+
- Express FRC and OXC in <i>E. coli</i> BL21 using pET28a
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+
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filtered out of the beer, haze and sediment may
+
−
 
+
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form<sup>4</sup>. In addition, calcium oxalate crystals
+
−
 
+
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can cause over-foaming during filling or when a
+
−
 
+
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pressurized container such as a can or bottle is
+
−
 
+
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opened<sup>4</sup>.<br><br>
+
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Deposits of beerstone provide protection and nutrients
+
−
 
+
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for bacteria to grow due to the porous surface of the
+
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+
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beerstone, into which nutrient-providing proteins often
+
−
 
+
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become entrapped<span class="super">6</span>. This allows
+
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+
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for unwanted microbial growth and the formation of
+
−
 
+
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biofilms upon the beerstone, for example, species of the
+
−
 
+
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genera <i>Pectinatus</i> and <i>Megasphaera</i>. These
+
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+
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microorganisms cause beer spoilage, products with reduced
+
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+
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shelf-life, off-flavours and sour tastes, rendering the
+
−
 
+
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beer unsuitable for sale or consumption thus resulting in
+
−
 
+
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financial loss to the brewer<span class="super">7</span>.
+
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+
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<i>Lactobacillus</i> species in beer, in particular,
+
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+
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causes high turbidity which manifests as a hazy
+
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+
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appearance in the liquid. It also causes a high level of
+
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+
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diacetyl in the beer, resulting in an unwanted ‘buttery’
+
−
 
+
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flavour<span class="super">7</span>. With the removal of
+
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+
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beerstone, growth of these microbial contaminants will be
+
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+
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prohibited, improving brew quality and reducing
+
−
 
+
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downstream processing. <br><br>
+
−
Beerstone is difficult to remove for several reasons.
+
−
 
+
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Calcium oxalate is extremely insoluble in both hot and
+
−
 
+
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cold water, meaning that the use of harsh chemicals is
+
−
 
+
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currently required for effective methods of removing
+
−
 
+
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beerstone. These involve caustic or other harsh cleaners
+
−
 
+
−
which are dangerous to work with due to the potential for
+
−
 
+
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exposure burns of the eyes and skin, and corrosive damage
+
−
 
+
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to surfaces<span class="super">2, 3, 8</span>. The use of
+
−
 
+
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these cleaning agents require long and frequent pauses in
+
−
 
+
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production which lower the efficacy of the brewing
+
−
 
+
−
process. Additionally, the equipment required to utilize
+
−
 
+
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these caustic chemicals and the chemical disposal
+
  
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requirements are costly and potentially environmentally
+
vector.
 +
- Assess the feasibility of using these enzymes as an
  
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damaging.  
+
alternate cleaning method to degrade beerstone.
 
</p>
 
</p>
  
−
<h1 class="descSub"><i>Oxalobacter formigenes</i> and the
+
<h1 class="descSub">Project Overview</h1>
  
−
Breakdown of Oxalate</h1>
 
 
<p class="descP">
 
<p class="descP">
−
<i>Oxalobacter formigenes</i> is an anaerobic, Gram-
+
<b>Step 1: Cloning of <i>frc</i> and <i>oxc</i> into DH5α
  
−
negative bacteria native to the human gut microbiota<span
+
</b><br>
 +
-Synthesize <i>frc</i> and <i>oxc</i><br>
 +
-Add PstI cut site to pET-28a <br>
 +
-Ligate <i>frc</i> and <i>oxc</i> into pET-28a <br>
 +
-Transform pET-28afrc/oxc into DH5α <br>
 +
<br>
 +
<b>Step 2: Clone <i>frc</i> and <i>oxc</i> into
  
−
class="super">5</span>.  <i>O. formigenes</i> is a safe
+
BL21</b><br>
 +
-Purify pET-28afrc/oxc from DH5α<br>
 +
-Transform pET-28afrc/oxc into BL21<br>
 +
<br>
 +
<b>Step 3: Express and Purify FRC and OXC</b><br>
 +
-Induce expression with IPTG and extract crude
  
−
(biosafety hazard level 1) organism that relies solely on  
+
proteins<br>
 +
-Purify proteins using Ni-NTA chromatography<br>
 +
<br>
 +
<b>Step 4: Characterize FRC and OXC</b><br>
 +
-Characterize enzyme function using Sodium Oxalate<br>
 +
-Characterize enzyme function using Calcium Oxalate<br>
 +
<br>
 +
<b>Step 5: Design a Cleaning Solution and Test on  
  
−
oxalate as its source of energy, as well as its main
+
Beerstone</b><br>
 +
-Test ability of enzymes to break down Beerstone<br>
 +
-Design a functional cleaning solution<br>
  
−
source of carbon<span class="super">5, 9</span>. 
 
−
 
−
Metabolism of oxalate is accomplished by two enzymes,
 
−
 
−
Formyl Coenzyme A Transferase (FRC) and Oxalyl-Coenzyme A
 
−
 
−
Decarboxylase (OXC)<span class="super">5, 10</span>.
 
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In the first reaction step, a Coenzyme A (CoA) is
 
−
 
−
transferred to oxalate by the FRC enzyme<span
 
−
 
−
class="super">10</span>.  It functions by forming a
 
−
 
−
ternary complex between the substrates and the enzyme,
 
−
 
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resulting in an oxalyl-CoA complex<span class="super">5,
 
−
 
−
10</span>.  The OXC enzyme then catalyzes a reductive
 
−
 
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reaction in which formyl-CoA and CO2 are produced<span
 
−
 
−
class="super">5, 10</span>.  The FRC enzyme then cycles
 
−
 
−
the CoA back to a new oxalate molecule to start the
 
−
 
−
process again<span class="super">5, 10</span>.  Thiamine
 
−
 
−
pyrophosphate (TPP), Mg2+, acetate, and CoA are required
 
−
 
−
for the reaction to take place<span class="super">5,
 
−
 
−
10</span>.  The reaction mechanism for the breakdown of
 
−
 
−
calcium oxalate by FRC and OXC can be shown by the
 
−
 
−
equations in Figure 1<span class="super">10</span>:
 
−
<br><br>
 
 
</p>
 
</p>
  
−
<h1 class="descSub">Our Project Design</h1>
 
−
 
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<p class="descP"> Here we will include information about
 
−
 
−
why we plan on doing our project the way we are, what our
 
−
 
−
plans are in some detail, and why we are doing what we
 
−
 
−
are doing this year<br><br>To be, or not to be: that is
 
−
 
−
the question:
 
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Whether ’tis nobler in the mind to suffer
 
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The slings and arrows of outrageous fortune,
 
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Or to take arms against a sea of troubles,
 
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And by opposing end them? To die: to sleep;
 
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No more; and by a sleep to say we end
 
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The heart-ache and the thousand natural shocks
 
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That flesh is heir to, ’tis a consummation
 
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Devoutly to be wish’d. To die, to sleep;
 
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To sleep: perchance to dream: ay, there’s the rub;
 
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For in that sleep of death what dreams may come
 
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When we have shuffled off this mortal coil,
 
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Must give us pause: there’s the respect
 
−
That makes calamity of so long life;
 
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For who would bear the whips and scorns of time,
 
−
The oppressor’s wrong, the proud man’s contumely,
 
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The pangs of despised love, the law’s delay,
 
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The insolence of office and the spurns
 
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That patient merit of the unworthy takes,
 
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When he himself might his quietus make
 
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With a bare bodkin? who would fardels bear,
 
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To grunt and sweat under a weary life,
 
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But that the dread of something after death,
 
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The undiscover’d country from whose bourn
 
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No traveller returns, puzzles the will
 
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And makes us rather bear those ills we have
 
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Than fly to others that we know not of?
 
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Thus conscience does make cowards of us all;
 
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And thus the native hue of resolution
 
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Is sicklied o’er with the pale cast of thought,
 
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And enterprises of great pith and moment
 
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With this regard their currents turn awry,
 
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And lose the name of action.–Soft you now!
 
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The fair Ophelia! Nymph, in thy orisons
 
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Be all my sins remember’d.</p>
 
−
 
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<h1 class="descSub">Future Development</h1>
 
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<p class="descP"> Here we will write about our plans for
 
−
 
−
the future of this project and what direction we plan on
 
−
 
−
heading. <br><br>To be, or not to be: that is the
 
−
 
−
question:
 
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Whether ’tis nobler in the mind to suffer
 
−
The slings and arrows of outrageous fortune,
 
−
Or to take arms against a sea of troubles,
 
−
And by opposing end them? To die: to sleep;
 
−
No more; and by a sleep to say we end
 
−
The heart-ache and the thousand natural shocks
 
−
That flesh is heir to, ’tis a consummation
 
−
Devoutly to be wish’d. To die, to sleep;
 
−
To sleep: perchance to dream: ay, there’s the rub;
 
−
For in that sleep of death what dreams may come
 
−
When we have shuffled off this mortal coil,
 
−
Must give us pause: there’s the respect
 
−
That makes calamity of so long life;
 
−
For who would bear the whips and scorns of time,
 
−
 
−
<h1 class="descSub">References</h1>
 
−
<p class="descRef"> Rose, D. This is a test (2017). Sci.
 
−
 
−
Awesome. 28-29 </p>
 
  
 
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<div class="column full_size">
 
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<h1>Design</h1>
 
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<p>
 
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Design is the first step in the design-build-test cycle
 
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in engineering and synthetic biology. Use this page to
 
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describe the process that you used in the design of your
 
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parts. You should clearly explain the engineering
 
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principles used to design your project.
 
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</p>
 
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<p>
 
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This page is different to the "Applied Design Award"
 
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page. Please see the <a
 
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href="https://2018.igem.org/Team:UofGuelph/Applied_Design"
 
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>Applied Design</a> page for more information on how to
 
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compete for that award.
 
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<div class="column two_thirds_size">
 
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<h3>What should this page contain?</h3>
 
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<ul>
 
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<li>Explanation of the engineering principles your team
 
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used in your design</li>
 
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<li>Discussion of the design iterations your team went
 
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through</li>
 
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<li>Experimental plan to test your designs</li>
 
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Revision as of 23:27, 6 December 2018

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Project Description

Background on Beerstone, FRC and OXC

Beerstone is a salt precipitate composed primarily of calcium oxalate (C2CaO4). It poses a large problem in the brewing industry due to its high insolubility and use of corrosive chemicals for its effective removal from brewing equipment1.

The reason for the high insolubility of beerstone is because one of its major components, calcium oxalate (C2CaO4), contains a chelator. Calcium ions in the water react with oxalic acids present in malt, forming calcium oxalate. When polypeptides found in beer are incorporated into the oxalate structure, the precipitate that is formed is known as beerstone2,3. Geographic regions that contain high levels of calcium in their drinking water, such as Guelph, Ontario, Canada, can lead to 165g of C2CaO4 buildup per 1000L batch of beer4. The porous nature of beerstone scale promotes biofilm formation from the microorganisms present in the brewing solution. Biofilm growth causes both “off flavours” that can ruin an entire batch of beer and also be a potential biosafety hazard for the consumer5.

Oxalobacter formigenes is a human gut bacterium that derives its energy solely from the metabolization of oxalate using enzymes Formyl-Coenzyme A Transferase (FRC) and Oxalyl-Coenzyme A Decarboxylase (OXC). Oxalate is brought into the cell by an oxalate-formate antiporter (OxIT) and converted to CO2 and formyl-CoA. The formyl- CoA is reused by FRC as a CoA donor in a subsequent reaction and released from the cell as formate by OxIT6.

Objectives

- Express FRC and OXC in E. coli BL21 using pET28a vector. - Assess the feasibility of using these enzymes as an alternate cleaning method to degrade beerstone.

Project Overview

Step 1: Cloning of frc and oxc into DH5α
-Synthesize frc and oxc
-Add PstI cut site to pET-28a
-Ligate frc and oxc into pET-28a
-Transform pET-28afrc/oxc into DH5α

Step 2: Clone frc and oxc into BL21
-Purify pET-28afrc/oxc from DH5α
-Transform pET-28afrc/oxc into BL21

Step 3: Express and Purify FRC and OXC
-Induce expression with IPTG and extract crude proteins
-Purify proteins using Ni-NTA chromatography

Step 4: Characterize FRC and OXC
-Characterize enzyme function using Sodium Oxalate
-Characterize enzyme function using Calcium Oxalate

Step 5: Design a Cleaning Solution and Test on Beerstone
-Test ability of enzymes to break down Beerstone
-Design a functional cleaning solution

University of Guelph iGEM 2018