Biosafety System Lac of Growth

Overview

Biosafety-System Lac of growth.

The Biosafety-System Lac of Growth <bbpart>BBa_K1172911</bbpart> is an improvement of the Biobrick <bbpart>BBa_K914014</bbpart> by changing the first promoter into the rhamnose promoter P_Rha and the integration of the alanine racemase <bbpart>BBa_K1172901</bbpart>. The transcription of the Barnase is regualted by the lac promoter and therefore LacI is used as repressor. The P_lac promoter is characterized by a high basal transcription so that there is a high lethality rate in this systems. But as there are different challenging opportunities to overcome this problem it is also an interesting Biosafety-System with a high potential use.

Genetic Approach

Rhamnose promoter P_Rha

The promoter P_Rha (<bbpart>BBa_K914003</bbpart>) naturally regulates the catabolism of the hexose L-rhamnose. The advantage of the operon for further usage is its solely positive regulation. The regulon consists of the promoter P_RhaT, which regulates the expression of the protein RhaT for the uptake of L-rhamnose and the two operons rhaSR and rhaBAD.
The operon rhaSR encodes the two transcriptional activators RhaS and RhaR, who are responsible for the positive activation of the L-rhamnose catabolism, while the operon rhaBAD encodes the genes for the direct catabolism of L-rhamnose.
When L-rhamnose is present, it acts as an inducer by binding to the regulatory protein RhaR. RhaR regulates his own expression and the expression of the regulatory gene rhaS by repressing or, in the presence of L-rhamnose, activating the operon rhaSR. Normally, the expression level is modest, but it can be enhanced by a higher level of intracellular cAMP, which increases in the absence of glucose. So, in the presence of L-rhamnose and a high concentration of intracellular cAMP, the activator protein RhaR is expressed on higher level, resulting in an activation of the promoter P_rhaT for an efficient L-rhamnose uptake and an activation of the operon rhaBAD. The L-rhamnose is than broken down into dihydroxyacetone phosphate and lactate aldehyde by the enzymes encoded by rhaBAD (Wickstrum et al., 2005).
A brief schematic summary of the regulation is shown in Figure 1.

Figure 1: The catabolism of L-rhamnose in E. coli is turned off in general but inducible by L-rhamnose. The induction activates the transcription of the genes rhaS and rhaR, which regulate the L-rhamnose catabolsim by positive activation of the rhamnose uptake (rhaT) and its metabolization (rhaBAD).

Dihydroxyacetone phosphate can be metabolized in the glycolysis pathway, while lactate aldehyde is oxidized to lactate under aerobic conditions and reduced to L-1,2,-propandiol under anaerobic conditions.
This degradation of L-rhamnose can be separated in three steps. In the first step the L-rhamnose is turned into L-rhamnulose by an isomerase (gene rhaA). L-rhamnulose is in turn phosphorylated to L-rhamnulose-1-phosphate by a kinase (gene rhaB) and the sugar phosphate is finally hydrolyzed by an aldolase (gene rhaD) to dihydroxyacetone phosphate and lactate aldehyde (Baldoma et al., 1988).
For our Safety-System Lac of Grwoth, the rhamnose promoter P_Rha is used to control the expression of the repressor AraC and the essential alanine racemase, because this promoter has an even lower basal transcription then the arabinose promoter P_BAD. This is needed to tightly repress the expression of the alanine racemase (alr) and thereby take advantage of the double-kill switch. Although the rhamnose promoter P_Rha is characterized by a very low basal transcription it can not be used for the control of the toxic RNase Ba (Barnase), which ist needed for the alanine racemase (alr), the other part of the double-kill switch. In conclusion this promoter is the best choice for the first part of the Biosafety-System, as it is tightly repressed in the absence of L-rhamnose, but activated in its presence.

Repressor LacI

Naturally the lacZYA operon encodes the genes for the direct catabolism of the disaccharide lactose in E. coli. The operon contains the lactose promoter P_lac and the genes for the catabolism of lactose to glucose and galactose. Upstream of the lac operator, in opposite orientiation, exists the coding sequence for the repressor LacI under the control of a weak promoter (Jacob et al., 1961).
Compared to the catabolism of the sugars L-rhamnose or L-arabinose, lactose, as a disaccharide has a higher energy content and is therefore used more preferable. Therefore the basal transcription of this promoter is even more higher. The leakiness of the lac promoter is thereby caused by the fact that LacY needs to be expressed for an efficient lactose uptake, while the uptake in the arabinose system is regulated separate (Görke et al., 2008).
In our Safety-System the LacI (<bbpart>BBa_C0012</bbpart>) is used for the repression of the lactose promoter P_lac.

Alanine racemase Alr

The alanine racemase Alr (EC 5.1.1.1) from the Gram-negative enteric bacteria Escherichia coli is a racemase, which catalyses the reversible conversion of L-alanine into the enantiomer D-alanine (see Figure 2). For this reaction the cofactor pyridoxal-5'-phosphate (PLP) is typically needed. The constitutive expressed alanine racemase (alr) is naturally responsible for the accumulation of D-alanine. This compound is an essential component of the bacterial cell wall, because it is used for the cross-linkage of peptidoglycan (Walsh, 1989).
The usage of D-alanine instead of a typically L-amino acid prevents cleavage by peptidases. However a lack of D-alanine causes to a bacteriolytic characteristics. In the absence of D‑alanine dividing cells will lyse rapidly. This fact is used for our Biosafety-Strain, a D-alanine auxotrophic mutant (K-12 ∆alr ∆dadX). The Biosafety-Strain grows only with a plasmid containing the alanine racemase (<bbpart>BBa_K1172901</bbpart>) to complement the D-alanine auxotrophy. Consequently the alanine racemase is essential for bacterial cell division. This approach guarantees a high plasmid stability, which is extremely important when the plasmid contains a toxic gene like the Barnase. In addition this construction provides the possibility for the implementation of a double kill-switch system. Because if the expression of the alanine racemase is repressed and there is no D-alanine supplementation in the medium, cells will not grow.

Figure 2: The alanine racemase (<bbpart>BBa_K1172901</bbpart>) from E. coli catalyses the reversible conversion from L-alanine to D-alanine. For this isomerisation the cofactor pyridoxal-5'-phosphate is necessary.

Terminator

Terminators are essential for the end of an operon. In procaryotes two types of terminators exist. The rho-dependent and the rho-independent terminator. Rho-independent terminators are characterized by their stem-loop forming sequence. In general, the terminator-region can be divided into four regions. The first region is GC-rich and constitutes one half of the stem. This region is followed by the loop-region and another GC-rich region that makes up the opposite part of the stem. The terminator closes with a poly uracil region, which destabilizes the binding of the RNA-polymerase. The stem-loop of the terminator causes a distinction of the DNA and the translated RNA. Consequently the binding of the RNA-polymerase is cancelled and the transcription ends after the stem-loop (Carafa et al., 1990).
For our Bioafety-System Lac of Growth the terminator is necessary to avoid that the expression of the genes under control of the rhamnose promoter P_Rha, like the Repressor AraC and the alanine racemase (alr) results in the transcription of the genes behind the arabinose promoter P_BAD, which contains the toxic Barnase <bbpart>BBa_K1172904</bbpart> and would lead to cell death.

Figure 3: Stem-loop structure of the terminator <bbpart>BBa_B0015</bbpart>, which is used for the Biosafety-System Lac of Growth. The terminator is used to make sure that solely both the repressor AraC and the alanine racemase Alr are expressed but the transcription of the toxic RNase Ba (Barnase) is avoided.

Lactose promoter P_lac

Naturally the lac operon encodes the genes for the direct catabolism of the disaccharide E. coli. The operon consists of a CAP-binding site, the lac promoter, the lac operator and the genes lacZ, lacY and lacA downstream of the promoter. The transcription of the lactose promoter is regulated by the LacI repressor, whose coding sequence is found upstream of the lacZYA operon under control of a weak promoter. In the absence of lactose the transcription of the genes behind the lactose promoter is blocked, caused by the binding of the lacI pressor. While in the presence of Lactose the repressor is released from the operator and the genes can be transcribed. Typically the transcription is enhanced by a high intracellular level of cAMP (Busby, 1999).

Figure 5:Structure of the lactose operon and its regulatory units. In the absence of lactose, transcription of the genes behind the lactose promoter is blocked. In the presens of Lactose a side reaction of the ß-Galactosidase (LacZ) synthesis allolactose, who causes a conformation change in the repressor LacI. The repressor LacI releases the operator sequnece and the transcription of the lactose operons starts.

The lactose promoter thereby regulates the transcription of the genes lacZ, lacY and lacA. The lacZ gene encodes for the ß-Galactosidase, a enzyme, who breaks down the lactose to glucose and galactose. The ß-Galactosidase catalyses additional the degradation from Lactose to Allolactose. By binding to the LacI repressor, Allolactose changes his conformation. So the repressor is not able to bind on the operator sequnece and so the transcription is not blocked any more. As only one enzyme is necessary to gain a substrate for the glycolysis is becomes clear, why the degradation of lactose is more preferable compared to L-arabinose or L-rhamnose.
To realize a preference of lactose, the transcription of the lactose promoter is not repressed as that strong. This is caused by the fact that the lacY gene, coding for the integral membrane protein lactose permease, is necessary for the lactose uptake and has to be transcripted on a low level.
The last gene of the lacZYA operon, lacA, encodes for a Transacetylase, who acetylizes glycosides that can not be metabolized. The acetylated glycosides are transported outside the cell to avoid their accumulation in the cell.
In our Biosafety-System the lac promoter is used for the regulation of the Barnase. As the lac promoter shows a high basal transcription, its might not ideal for the regulation of a toxic gene product, but the Biosafety-System Lac of growth is ideal for comparison with the other Systems to measure the level of basal transcription under repressed and unrepressed conditions. Besides we improved the leakiness of the lactose promoter by adding a second lacI-binding site 12 nt downstream of the excisting bining site. As this distance corresponds to about one helix turn of the double helix, this should allow an additional LacI repressor to bind on the other site of the DNA and tighten the repression of the lactose promoter. Unfortunately the improvement of the so called double lac promoter could not be quantified, because lac of time (Lewis, 2005).

Barnase

The Barnase (EC 3.1.27) is an 12 kDa extracellular microbial ribonuclease, which is naturally found in the gram-positive soil bacteria Bacillus amyloliquefaciens and consist a single chain of 110 amino acids. The Barnase (RNase Ba) catalyses the cleavage of single stranded RNA, where the hydrolysis of the dinucleotides has the highest affinity to the structure GpN. In the first step of the RNA-degradation a cyclic intermediate is formed by transesterification and afterwards this intermediate is hydrolysed yielding in a 3'-nucleotide (Mossakowska et al., 1989).

Figure 8: Chemical reaction of the RNA-cleavage by the RNase Ba. First the transesterifiaction by the Glu-73 residue is performed and then this cyclic intermediat is hydrolized by the His-102 of the Barnase.

In Bacillus amyloliquefaciens the activity ot the Barnase (RNase Ba) is inhibited intracelluar by the Inhibitor called barstar. Barstar consists only about 89 amino acids and binds with a high affinity to the toxic Barnase. This prevents the cleavage of the intracellular RNA in the host organism (Paddon et al., 1989). Therefore the Barnase acts naturally only outside the cell and is translocated under natural conditions. For the Biosafety-System we tried to modified this aspect by cloning only the sequence responsible for the cleavage of the RNA, but not the part of the native Barnase, which is essential for the extracellular transport.
As shown in the graphic below, the transcription of the DNA, which encodes the Barnase produces a 474 nt RNA. The translation of the RNA of this ribonuclease starts about 25 nucleotides downstream from the transcription start and can be divided into two parts. The first part (colored in orange) is translated into a signal peptide at the N-Terminus of the Barnase. This part is responsible for the extracellular translocation of the RNase Ba, while the peptide sequence for the active Barnase starts 142 nucleotides downstream from the transcription start (colored in red).
For the Biosafety-System we used only the coding sequence (<bbpart>BBa_K1172904</bbpart>) of the Barnase itself to prevent the extracellular translocation of the toxic gene product. This leads to a rapid cell death if the expression of the Barnase isn't repressed by the repressor of the Biosafety-System.

Figure 9: Sequence of the Signalpeptide in front of the RNase Ba (Barnase). The Biobrick <bbpart>BBa_K1172904</bbpart> does not consist the signal sequence for the extracellular translocation, but only the coding sequence for the mature enzyme.

Biosafety-System Lac of growth

Together with the Biosafety-Strain K-12 ∆alr ∆dadX the Biosafety-System Lac of Growth takes advantage of this genes by combine them to a powerful device, which allows to control the bacterial cell division. The control of the bacterial growth is thereby active and passive possible. Active by inducing the lactose promoter with L-arabinose and passive by the induction of L-Rhamnose. The passive control makes it possible to control the bacterial cell division in an defined environment, like the MFC by adding continously L-Rhamnose to the media. As shown in the figure below, this leads to an expression of the essential Alanine-Racemase (alr) and the lacI repressor, so that the expression of the RNase Ba is repressed.

Figure 10: Biosafety-System Lac of Grwoth in the presens of L-Rhamnose. The essentail Alanine-Racemase (alr) and the repressor araC are expressed, so that the expression of the RNAse Ba is repressed and the Bacteria grow.

When the bacteria exit the defined environment of the MFC or L-Rhamnose is not added any more to the media, the expression of the Alanine-Racemase (alr) and the lacI repressor decreases, so that the expression of the toxic RNase Ba (Barnase) is not inhibted so strong any more. The cleavage of the intracellular RNA by the Barnase and ideally also the lack of synthesized D-alanine, caused by the repressed Alanine-Racemase inhibits the cell division and makes sure that the bacteria can only grow in the defined area.

Figure 11: Biosafety-System Lac of growth outside the defined conditions and a decreased concentration of L-Rhamnose. The expression of the Alanine-Racemase and lacI repressor is reduced and ideally completly shutdown. In contrast the expression of the RNase ba (Barnase) is sligthly turned on, leading to cell death by RNA cleavage.

Results

Characterization of the lactose promoter plac

First of all the bacterial growth under the pressure of the unrepressed lactose promoter plac was investigated on different carbon source. Therefore the cultivation on M9 minimal media with Glucose or Glycerol was characterized. To identify the transcription rate of the unrepressed lactose promoter plac the expression of the green fluorescence protein GFP <bbpart>BBa_E0040</bbpart> behind the plac promoter was used.
As shown in figure 12 below, the bacteria adapted better on glucose then on Glycerol. As glucose is the more powerful energy source, because it posses more carbon atoms than glycerol these result was expected before. So more interesting are the fluorescence measurement shown in the figure 13. As it can be seen also the fluorescence depends on the carbon source, but not as strong as it can be seen by the arabinose promoter pBAD.
This can be explained by the fact that glucose itself also represses the lactose promoter, while glycerol does not and in comparision to the arabinose system the lactose promoter is known to be more leaky. So in the presence of glucose the intracellular concentration of cAMP is low and represses the inefficient catabolism of lactose, so that the glucose is catabolized first by the bacteria resulting in an optimal growth. In the absence of glucose the concentration of cAMP increases, which enhances the transcription of the most operons, who regulate the enzymes for the catabolism of an alternative carbon source. Therefore the expression of GFP under the control of the lactose promoter decreases on glycerol.

Figure 12: Characterization of the bacterial growth of the lactose promoter with GFP (<bbpart>BBa_E0040</bbpart>) in the Biosafety-Strain K-12 ∆alr ∆dadX. The M9 media was supplemented with 5 mM D-alanine. It can be seen, that the bacteria grow faster on M9 minimal media glucose than on M9 minimal media glycerol.

Figure 13: Characterization of the fluorescence of lac promoter with GFP (<bbpart>BBa_E0040</bbpart>) in the Biosafety-Strain K-12 ∆alr ∆dadX. The bacteria were cultivated on M9 minimal media with 5 mM D-alanine supplemented

So it can be seen that the building of GFP differs between the cultivation on glucose and the cultivation of glycerol. As the production rate by using glucose as carbon source is always beneath the cultivation with glycerol, this impacts that the expression of GFP under the control of the lac promoter is more repressed in the presence of glucose. As the specific production rate was calculated between every single measurement point the curve is not smoothed and so the fluctuations have to be ignored, as they do not stand for are real fluctuations in the transcription in the expression of GFP. They are caused by the growth curve and the fluorescence curve. And as they are not ideal there exists the fluctuations. But this graph shows clearly the difference between the two carbon sources.

Figure 14: Specific growth rate of GFP behind the pBAD promoter by the use of different carbon sources.

Characterization of the Biosafety-System Lac of growth

The Biosafety-System Lac of Growth was characterized on M9 minimal medium with glycerol as carbon source. As for the characterization of the pure lactose promoter above, the bacterial growth and the fluorescence of GFP <bbpart>BBa-E0040</bbpart> was measured. Therefore the wild type and the Biosafety-Strain E. coli K-12 ∆alr ∆dadX were cultivated once with the induction of 1% L-Rhamnose and once only on glycerol.
First of all it is obviously shown in figure 15 that the growth of the bacteria, who are induced with 1 % L-Rhamnose (blue and black curve) is significant slower than on pure glycerol (orange and red curve). This is attributed to the high metabolic pressure of the induced bacteria. The expression of the repressor lacI and the Alanine-Racemase (alr) simultaneously causes a high outlay of the cells so that they grow slower then the uninduced cells, who expresses only GFP. Additional the lactose promoter is tightly regulated, so that the expression even with a small amount of the repressor lacI is not that high and therefore not as stressful.
Comparing the bacterial growth with the fluorescence in figure 16 it can be seen that the fluorescence of the Biosafety-Strain can not be evaluate because of the long duration of the lac-phase, but the wild-type shows a figure that is comparable with the bacterial growth.

Figure 15: Characterization of the bacterial growth of the Biosafety-System on M9 minimal media glycerol. The figure compares the wild tpye k-12 and the Biosafety-Strain K-12 ∆alr ∆dadX and the induction by L-Rhamnose to pure glycerol.

Figure 16: Characterization of the fluorescence of the Biosafety-System Lac of Growth. The figure compares the wild tpye k-12 and the Biosafety-Strain K-12 ∆alr ∆dadX and the induction by L-Rhamnose to pure glycerol.

From the figure above it can not be seen if the expression of the repressor lacI does effect the transcription of GFP or not. The slower growth of the bacteria is a first indication that the repressor lacI and the Alanine-Racemase are highly expressed, but as the growth of the bacteria shows nearly the same figure than the fluorescence it could be possible that the repressor does not effect the expression level of GFP under the control of the lactose promoter . That the Biosafety-System works as aspected by repressing the expression of GFP in the presence of L-Rhamnose can be seen from figure 18 below. The calculated specific production rate (equation 1) differs, so that the production of GFP in the presence of L-Rhamnose is always lower than in its absence.
As the specific production rate was calculated between every single measurement point the curve is not smoothed and so the fluctuations have to be ignored, as they do not stand for are real fluctuations in the transcription in the expression of GFP. They are caused by the growth curve and the fluorescence curve. And this measured curves are not ideal the calculation of the specific production rate causes the fluctuations. But it can be seen very clear that the production of GFP differ an is much lower, when the bacteria are induced with 1% L-Rhamnose. So the Biosafety-System Lac of Growth works.

Figure 17: Specific production rate, calculated by equation (1). The production rate of GFP of the uninduced bacteria is higher compared to the bacteria induced with 1% L-Rhamnose. The Biosafety-System AraCtive works.

Conclusion of the Results

As the expression level of GFP is increased in the absence of L-Rhamnose and decreased in its presence, the Biosafety-System Lac of Growth works as aspected. In figure 18 the specific production rates after 7,5 hours are compared. It can be seen that the expression level of the lac promoter decreases in the uninduced Safety-Strain compared to the uninduced second part of the Biosafety-System and that the induction with L-Rhamnose leads to a tight repression of the transcription and therefore the expression of GFP.

Figure 18: Comparision of the specific production rate of GFP in the with L-Rhamnose induced Biosafety-System Lac of Growth, the uninduced Biosafety-System Lac of Growth and the second part of the Biosafety-System (pLac-GFP only).

References

• Baldoma L and Aguilar J (1988) Metabolism of L-Fucose and L-Rhamnose in Escherichia coli: Aerobic-Anaerobic Regulation of L-Lactaldehyde Dissimilation [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC210658/pdf/jbacter00179-0434.pdf|Journal of Bacteriology 170: 416 - 421.].

• Busby S, Ebright RH (1999) Transcription activation by catabolite activator protein (CAP).[http://ac.els-cdn.com/S0022283699931613/1-s2.0-S0022283699931613-main.pdf?_tid=a8f22b74-2cf4-11e3-9457-00000aab0f6c&acdnat=1380891687_f17fd24e5a3e15da96493226fdcaaa10|Journal of molecular biology 239: 199 - 213.].

• Carafa, Yves d'Aubenton Brody, Edward and Claude (1990) Thermest Prediction of Rho-independent Escherichia coli Transcription Terminators - A Statistical Analysis of their RNA Stem-Loop Structures [http://ac.els-cdn.com/S0022283699800059/1-s2.0-S0022283699800059-main.pdf?_tid=ede07e2a-2a92-11e3-b889-00000aab0f6c&acdnat=1380629809_2d1a59e395fc69c8608ab8b5aea842f7|Journal of molecular biology 3: 835 - 858].

• Görke, Boris and Stülke, Jörg (2008) Carbon catabolite repression in bacteria: many ways to make the most out of nutrients [http://www.nature.com/nrmicro/journal/v6/n8/full/nrmicro1932.html|Nature Reviews Microbiology 6: 613 - 624].

• Jacob, F Monod J (1961) Genetic regulatory mechanisms in the synthesis of proteins. [http://www.ncbi.nlm.nih.gov/pubmed/13718526|Journal of molecular biology 216: 318 - 356].

• Lewis, Mitchell (2005) The lac repressor [http://www.sciencedirect.com/science/article/pii/S1631069105000685|Comptes rendues biologies 328: 521 – 548].

• Mossakowska, Danuta E. Nyberg, Kerstin and Fersht, Alan R. (1989) Kinetic Characterization of the Recombinant Ribonuclease from Bacillus amyloliquefaciens (Barnase) and Investigation of Key Residues in Catalysis by Site-Directed Mutagenesis [http://pubs.acs.org/doi/pdf/10.1021/bi00435a033|Biochemistry 28: 3843 - 3850.].

• Paddon, C. J. Vasantha, N. and Hartley, R. W. (1989) Translation and Processing of Bacillus amyloliquefaciens Extracellular Rnase [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC209718/pdf/jbacter00168-0575.pdf|Journal of Bacteriology 171: 1185 - 1187.].

• Voss, Carsten Lindau, Dennis and Flaschel, Erwin (2006) Production of Recombinant RNase Ba and Its Application in Downstream Processing of Plasmid DNA for Pharmaceutical Use [http://onlinelibrary.wiley.com/doi/10.1021/bp050417e/pdf|Biotechnology Progress 22: 737 - 744.].

• Walsh, Christopher (1989) Enzymes in the D-alanine branch of bacterial cell wall peptidoglycan assembly. [http://www.jbc.org/content/264/5/2393.long|Journal of biological chemistry 264: 2393 - 2396.]

• Wickstrum, J.R., Santangelo, T.J., and Egan, S.M. (2005) Cyclic AMP receptor protein and RhaR synergistically activate transcription from the L-rhamnose-responsive rhaSR promoter in Escherichia coli. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251584/?report=reader|Journal of Bacteriology 187: 6708 – 6719.].