Difference between revisions of "Team:BNU-CHINA/Module"

Line 150: Line 150:
 
                     </ul>
 
                     </ul>
 
<br/>
 
<br/>
 +
<hr/>
 +
 +
<h3>3.  Suicide</h3>
 +
<h4>1.  Background</h4>
 +
                    <p>In nature, some of the bacterial cells sense the density of their population through a sophisticated cell–cell communication system. When the cell density reaches a specific threshold and the signal molecules accumulate reaches a certain concentration, they will do a series of measures to regulate their group behavior. For example, they can trigger the expression of various genes to induce apoptosis to decrease the population density. So the amount of population will keep dynamic balance. The phenomenon above is called quorum sensing.
 +
                    </p>
 +
                    <p>Referring the research did by Lingchong You[1] and using the quorum sensing principle, we constructed a genetic circuit controlling the population density of the engineering bacteria regulated by human.
 +
                    </p>
 +
<br/>
 +
 +
<h4>2.  AHL luxI luxR MazF</h4>
 +
                    <p>N-acyl-homoserine lactone(AHL) is a signalling molecular found by Vibrio fischeri which can diffuse freely through cell membrane. Luxl, which is the expression product of the luxl gene, can catalyze the synthesis of the AHL inside the cell at a certain rate. AHL then diffuses outside the cell. And the expression product of luxR is LuxR. At sufficiently high concentrations, it binds with AHL to become a LuxR-AHL complex and it can also activates the LuxR transcriptional regulator, which in turn induces the expression of a killer gene (E) under the control of a luxI promoter (pluxI)15). But lux pR does not have promoter activity without LuxR-AHL complex.
 +
                    </p>
 +
                    <p>The toxic protein MazF expressed by mazF gene is a nonspecific ribonuclease. It can freely and specifically shear the ACA sequence of mRNA to inhibit the synthesis of the protein. So the growth of cells will stop.
 +
                    </p>
 +
<br/>
 +
 +
<h4>3. Design</h4>
 +
                    <ul>
 +
                        <li>
 +
                            <p>upstream: the production of LuxR and AHL We linked the RBS, the constitutive promoter(BBa_J23100), Lux(BBa_C0062) and LuxI(BBa_C0061) in order. So during the growth of the bacteria, they will product the AHL and LuxR constantly.</p>
 +
                        </li>
 +
                        <li>downstream: the starting of the luxpR and the expression of the toxic protein MazF When the concentration of the AHL around reaches a specific threshold, it will bind with LuxR to become a LuxR-AHL complex to activate the luxpR promoter. And then the expression of the mazF gene at downstream will start. The MazF will lead to the apoptosis. So the population density will decrease.
 +
                        </li>
 +
                        <figure class="text-center">
 +
                            <img src="#" alt="Loss the Fig" />
 +
                            <figcaption>Fig.6 After nematodes ate the bacteria with rMpL
 +
                            </figcaption>
 +
                        </figure>
 +
                    </ul>
 +
<br/>
 +
<hr/>
 +
 
</html>
 
</html>
 
{{BNU-CHINA/article/end}}
 
{{BNU-CHINA/article/end}}

Revision as of 17:57, 14 September 2015

Team:BNU-CHINA - 2015.igem.org

1. Bait

Nematode has been up to over 5000 of 200 genus[1]. Among them, over 100 species of nematodes are damaging the agricultural, forestal and economic crops of China who widely parasitize the roots, stems, leaves, flowers, buds and seeds of manifold plants, harming the development of agriculture and forestry seriously.

A newest research by USA indicates that the plant-parasitic nematodes damage leads to about 8 billion dollars’ losses to their croppers, which takes 12% of the whole value of the crop output. Meanwhile, according to incomplete statistics, the losses caused by paratrophy nematodes can reach 100 billion every year worldwide[2]. China’s researchers have done some relevant surveys as well, and according to incomplete statistics, 17 provinces such as Anhui, Hainan, Hubei, Gansu, Zhejiang and Fujian have reported root knot nematode disease once, among which the morbidity of some severe regions in Shandong province can up to 2/3[3]. Therefore we can note that plant-parasitic nematodes have brought out severe lost to global agriculture and forestry already.


2. Killer

2.1 Bace 16

    Backgrounds
  • Bacillus nematocida

    • A novel bacterial strain named bacillus nematocida has been isolated from soil in Yunnan, China by Huang Xiaowei in 2005. It’s an endospore-forming and Gram-positive bacterium. It can lure nematodes by emitting potent volatile organic compounds, and once the bacterium enter the intestine of nematodes, it can secrete proteases with broad substrate ranges but preferentially target essential intestinal proteins, leading to nematode death. Up till now, the research group has found that B. nematocida has remarkable nematotoxic activity against Panagrellus redivivus, which is a kind of free-living nematode, and Bursaphelenchus xylophilus, which are parasitic on the xylem of the pines.

    Loss the Fig
    Figure 1. Microscopic examination of B.nematocida strain B 16 target sites.

    (A) B oth the in te stine and cuticle of n em atodes we re inta ct when treate d w ith E. coli .(B) Structures of pharynx, muscle, and intestine were disorganized when treated with B. nematocidastra in B1 6. (C) Nematodes in the E. coli-treated control group had sm oo th undisturbe d surfaces w ith a healthy cuticle structure tha t included the regu la r stria e a nd lateral lines. (D) Nematodes infected with B. nematocidastrain B16 showed a lightly exfoliated cuticle. (E) The cross-section of an untreated, healthy nematode showed a highly ordered and compact intestinal structure. (F)Thecross-section of a nematode infected with B. nematocida stra in B1 6 showe d n um erou s d efects in clud ing fusio n, vesiculation , a nd lo osening o f v ario us orga ns. (G)Low-magnification TEM of the midgut of the control nematode showed ordered, densely arrayed, and normal-looking microvilli. (H) Microvilli in strain B16-infected nematodes appeared destroyed with signi ficant membrane-tethering defects. Arrows indicate healthy (G) and damaged (H) and microvilli.

  • The processes for B. nematocida to kill nematodes

    • After Bacillus nematocida was isolated and testified for its nematotoxicity, the mechanism of the infection process of this strain has been explored, and its pathogenesis against nematodes was said to be a Trojan horse mechanism.

    First, B. nematocida has a simple but effective strategy for attracting nematodes, it can use a mixture of VOCs as the lure in a kill-from-within nematocidal strategy.

    Once inside the worm, the bacterium colonizes the intestinal tract of the C. elegans and secretes extracellular proteases that kill the nematodes primarily through damage to the intestine of its host.

    A serine protease bace16 was first reported as a pathogenic factor against nematodes, whose accession number is AY708655. It was identified by methods such as ammonium sulfate precipitation. [1] In vitro assay demonstrated that the recombinant protease Bace16 expressed in Escherichia coli presented a nematotoxic activity, and it has been verified by experiments that Bace16 has the ability to degrade a nematode cuticle, leading to the nematode’s death.[3] To our knowledge, the nematode cuticle mainly consists of keratin, collagen, and fibers, which made it a rigid but flexible multilayered extracellular exoskeleton and a necessary barrier to prevent nematodes from damages.[2] So Bace16 could be considered as a core component of this project to kill the nematode.


    Bace 16
  • Structure

    • The molecular mass of a mature Bace16 protein is about 28kDa. And the protein has 275 residues, with a catalytic triad center containing His, Asp, and Ser residues and two calcium binding sites for stabilizing the three-dimensional structure. Characterization of the purified protease revealed the optimum activity of Bace16 is at pH10, 50℃. The deduced protein also contains a presequence signal peptide of 30 amino acids and a propeptide of 77 amino acids. The presequence signal peptide directs the secretion of subtilisin from the interior of cells, while the propeptide functions as a chaperon to facilitate the folding process of the active protease.[4] By sequence alignment, researchers found that the whole amino acid residues of Bace16 showed only around 33% sequence identity between cuticle-degrading proteases produced by several fungi such as Beauveria bassiana, Cordyceps brongniartii, Metarhizium anisopliae, etc. And only several residues near the conserved catalytic triad that are probably essential for activity of cuticle degradation are in consensus in all the proteases. However, Bace16 and other subtilisins produced by several bacteria are found 62-98% homologous, much higher than relevant fungi. Besides, the deduced amino acids of Bace16 has 98% identity with subtilisin BPN’ from B. amyloliquefaciens. So the enzyme probably belongs to the subtilisin family of enzymes, subtilisin BPN’ (EC 3.4.21.14, also known as Novo, or Nagarse), based on the alignment of the amino acid sequence in NCBI.[5]

  • Function

    • According to relevant research, Bace16 is the key reason for the high infection toxicity of bacillus nematocida to Panagrellus redivivus. Bioassay with purified Bace16 has showed that 90% of the nematodes could be killed within 24 h at the concentration of 1.79 μg/ml; after 48 h, all of the tested nematodes were almost killed and degraded.[5] Researchers found that recombinant protease rm-Bace16(whose molecular weight is 34kDa) expressed in Escherichia coli also presented a nematotoxic activity. And both Bace16 and rm-Bace16 could degrade a broad range of substrates including casein, denatured collagen, and nematode cuticle. In addition, the corresponding extract of the B. nematocida strain with a bace16 knockout mutant decreased significantly proteolytic activity and nematotoxic activity compared with both rm-Bace16 and the wild-type strain under various physiological conditions. [3] And the table[3] below compares the proteolytic activities between wild strain, recombinant strain and bace16 mutant.

    Due to the complicated renaturation process of recombinant protein, the conformation of Rm-Bace16 has some differences, so the enzyme activities are always lower than Bace16, but it still has significant nematotoxity comparing to Bace16 extract. And the research has set a precedent of expressing Bace16 in engineering bacteria for us to refer.


    Why we choose E. coli expressing bace16 to kill nematodes ?
  • the needs for biocontrol agents

    • Plant-parasitic nematodes cause serious losses to a variety of agricultural crops worldwide. Since the traditional methods based on the use of nematocides and antihelminthic drugs are associated with major environmental and health concerns, the development of biocontrol agents of control nematodes is of major importance [6].

  • Bacteria are easy to culture

    • Bacteria are suitable for their rapid culturing and production compared with fungi, which has been used extensively as bioinsecticides against nematodes in soil. And E. coli is especially easy to culture and conduct gene manipulation in the lab stage.

  • Protease is widely used for killing nematodes

    • A common group of virulence factors shared among bacterial pathogens are the proteases, and the primary function of proteases in the bacterial kingdom is to provide a source of free amino acids for bacterial survival and growth, but there is accumulating evidence that proteases also play a role in bacterial pathogenesis during the invasion and destruction of host tissues. The prevalent view regarding the mode of action of the extracellular proteases during nematode infection is that these proteases participate in cuticle penetration. So we choose a serine protease Bace16 in our project to kill nematodes, meanwhile, protease is easy to express in bacteria.


2.2 rMpL

  • agarose gel electrophoresis of rMpL

    • First, we did restriction endonuclease analysis to test if we had successfully synthesized rmpl gene with pBAD promoter(BBa_K206000) in its upstream region.We digested the plasmid with restriction enzymes EcoRI and PstI. Then we did agarose gel electrophoresis(AGE) and found that the plasimd was digested into two fragments, one of which was about 700bp long, as we expected(Fig.1). It proves that we have successfully built the vector rMpL-pSB1C3 as we planned earlier.

    Loss the Fig
    Fig.1 the agarose gel electrophoresis of gene rMpL, the bands pointed by arrows represent rMpL genes.Lane M,DNA marker; Lane 1-4, rMpL-pSB1C3 plasmids digested by EcoRI and PstI. sites.

    What’s more, we have built another vector including rMpL gene. The backbone of this vector is also pSB1C3, but the promoter of rMpL has been changed into a constitutive promoter(BBa_J23100). We also did restriction endonuclease analysis on this vector either. The agarose gel electrophoresis figure shows that we successfully built this part too.


  • SDS-PAGE

    • After we successfully built the vectors, we transferred the vectors into different E.coli strains depending on the kinds of vectors .Vectors with pBAD promoter were transferred into E.coli BW25113 and vectors with constitutive promoter were transferred into E.coli BL21 to express rMpL protein respectively. After rmpl gene was expressed in the bacteria, we did SDS-PAGE to testify the expression of rMpL protein. And according to the SDS-PAGE figure, we expressed rMpL in both kinds of E.coli strains.(Fig.2,3)

    Loss the Fig
    Fig.2 SDS-PAGE of rMpL

    Lane 1, molecular weight standards (kDa); lane 2-5, supernatant after 1.2, 1.2, 1.0, 1.0 uM L-Ara induction respectively; lane 7, supernatant after 0 uM L-Ara induction. Lane 8: supernatant of the pSB1C3; Lane 9,10,12,13,14: homogenate after 1.2, 1.2, 1.0, 1.0, uM L-Ara induction respectively; lane 15: homogenate of the pSB1C3.

    Loss the Fig
    Fig.3 SDS-PAGE of rMpL (constitutive promote ) decoloration for five hours
    Loss the Fig
    Fig.4 SDS-PAGE of rMpL (constitutive promoter) decoloration for ten hours

  • Nematoxicity Test

    • At last, we did nematoxicity test to find if rMpL protein did be able to prevent C.elegans from developing to adulthood from lava. And as we showed in the microscopic figures below, nematodes treated with recombinant bacteria show significant difficulty in developing to adulthood, such as the length of the nematodes and the. While the control group show the opposite reaction, the worms can develop to adulthood normally. And as for the motility of the nematodes, the nematodes which ate the bacteria expressed rMpL moved slower than the control group. The following figures shows the differences between the experimental groups and the control groups.

    Loss the Fig
    Fig.5 After nematodes ate the bacteria only with pSB1C3
    Loss the Fig
    Fig.6 After nematodes ate the bacteria with rMpL

  • Discussion

    • During our experiment, we found an interesting phenomenon. When we changed our pBAD promoter to constitutive promoter, the growth of the E.coli became much slower. Here are the pictures. pSB1C3-BW25113 is the bacteria with the pBAD promoter and the pSB1C3-BL21 is the bacteria with constitutive promoter. We can easily find the difference.

    Loss the Fig
    Fig.7 Cultivating for 5 hours
    Loss the Fig
    Fig.8 Cultivating for 10 hours

    We think it maybe because rMpL could do harm to the E.coli themselves. So it verifies that the pBAD promoter is more suitable than constitutive promoter.


3. Suicide

1. Background

In nature, some of the bacterial cells sense the density of their population through a sophisticated cell–cell communication system. When the cell density reaches a specific threshold and the signal molecules accumulate reaches a certain concentration, they will do a series of measures to regulate their group behavior. For example, they can trigger the expression of various genes to induce apoptosis to decrease the population density. So the amount of population will keep dynamic balance. The phenomenon above is called quorum sensing.

Referring the research did by Lingchong You[1] and using the quorum sensing principle, we constructed a genetic circuit controlling the population density of the engineering bacteria regulated by human.


2. AHL luxI luxR MazF

N-acyl-homoserine lactone(AHL) is a signalling molecular found by Vibrio fischeri which can diffuse freely through cell membrane. Luxl, which is the expression product of the luxl gene, can catalyze the synthesis of the AHL inside the cell at a certain rate. AHL then diffuses outside the cell. And the expression product of luxR is LuxR. At sufficiently high concentrations, it binds with AHL to become a LuxR-AHL complex and it can also activates the LuxR transcriptional regulator, which in turn induces the expression of a killer gene (E) under the control of a luxI promoter (pluxI)15). But lux pR does not have promoter activity without LuxR-AHL complex.

The toxic protein MazF expressed by mazF gene is a nonspecific ribonuclease. It can freely and specifically shear the ACA sequence of mRNA to inhibit the synthesis of the protein. So the growth of cells will stop.


3. Design

  • upstream: the production of LuxR and AHL We linked the RBS, the constitutive promoter(BBa_J23100), Lux(BBa_C0062) and LuxI(BBa_C0061) in order. So during the growth of the bacteria, they will product the AHL and LuxR constantly.

  • downstream: the starting of the luxpR and the expression of the toxic protein MazF When the concentration of the AHL around reaches a specific threshold, it will bind with LuxR to become a LuxR-AHL complex to activate the luxpR promoter. And then the expression of the mazF gene at downstream will start. The MazF will lead to the apoptosis. So the population density will decrease.
    • Loss the Fig
    Fig.6 After nematodes ate the bacteria with rMpL