Difference between revisions of "Part:BBa K5398630"
Line 1: Line 1:
 
__NOTOC__
 
__NOTOC__
 
<partinfo>BBa_K5398630 short</partinfo>
 
<partinfo>BBa_K5398630 short</partinfo>
 +
 +
<p>LicV is a fusion protein, which could be activated with blue light. It consists of the N-terminal RNA-binding domain (coantiterminator, CAT) of LicT and Vivid(VVD) which is a small LOV domain-containing protein. When induced by blue light, VVD dimerizes and leads to the conformational changes of LicT, thus stabilizing the LicT dimer and specifically binding a ribonucleic antiterminator (RAT) RNA sequence to prevent the formation of an RNA terminator stem–loop structure.</p>
 +
 +
===Introduction===
 +
<p>EL222 is a natural photosensitive DNA-binding protein that dimerizes and binds DNA upon blue light exposure. It is composed of a N-terminal light-oxygen-voltage(LOV) domain and a C-terminal helix-turn-helix(HTH) DNA-binding domain characteristic of LuxR-type DNA-binding proteins. EL222 could act as a transcriptional activator in a tunable blue light-inducible promoter system. pBlind, a synthetic blue light-inducible promoter, is formed by replacing the lux box which is a 20-bp inverted repeat from the luxI promoter with the 18-bp EL222 binding protein region. When exposed to blue light, EL222 dimerizes and overlaps the -35 region of the promoter thus recuiting RNAP. But a high leakage level of this blue light-induced system is witnessed. Aiming to lower the leakage, XMU-China 2021 replaced the strong promoter BBa_J23106 with pBlind. Although the leakage issue has improved somewhat, a quantity of reporter genes will still be expressed without blue light. </p>
 +
 +
<html lang="zh">
 +
<head>
 +
    <meta charset="UTF-8">
 +
    <meta name="viewport" content="width=device-width, initial-scale=1.0">
 +
    <style>
 +
        .module {
 +
            border: 1px solid #ccc; /* 边框 */
 +
            padding: 20px; /* 内边距 */
 +
            margin: 20px auto; /* 外边距，自动居中 */
 +
            width: 500px; /* 模块宽度 */
 +
            text-align: center; /* 内容居中 */
 +
            box-shadow: 0px 0px 10px rgba(0, 0, 0, 0.1); /* 阴影效果 */
 +
        }
 +
    </style>
 +
</head>
 +
<body>
 +
    <div class="module">
 +
        <img src="https://static.igem.wiki/teams/5398/improvement/t-xmu-china-k3739064-k3739064-pet28a-regular-pcr.webp" width="400" height="auto" alt="Original EL222 system">
 +
        <p><b> Fig. 1 | EL222 system designed by XMU-China 2021 </b></p>
 +
    </div>
 +
</body>
 +
</html>
 +
 +
<p>LicV is a fusion protein, which could be activated with blue light. It consists of the N-terminal RNA-binding domain (coantiterminator, CAT) of LicT and Vivid(VVD) which is a small LOV domain-containing protein. When induced by blue light, VVD dimerizes and leads to the conformational changes of LicT, thus stabilizing the LicT dimer and specifically binding a ribonucleic antiterminator (RAT) RNA sequence to prevent the formation of an RNA terminator stem–loop structure.</p>
 +
 +
<html lang="zh">
 +
<head>
 +
    <meta charset="UTF-8">
 +
    <meta name="viewport" content="width=device-width, initial-scale=1.0">
 +
    <style>
 +
        .module {
 +
            border: 1px solid #ccc; /* 边框 */
 +
            padding: 20px; /* 内边距 */
 +
            margin: 20px auto; /* 外边距，自动居中 */
 +
            width: 500px; /* 模块宽度 */
 +
            text-align: center; /* 内容居中 */
 +
            box-shadow: 0px 0px 10px rgba(0, 0, 0, 0.1); /* 阴影效果 */
 +
        }
 +
    </style>
 +
</head>
 +
<body>
 +
    <div class="module">
 +
        <img src="" width="400" height="auto" alt="Improved EL222 system">
 +
        <p><b> Fig. 2 | Improved EL222 system with <i>LicV</i> and <i>RAT</i> </b></p>
 +
    </div>
 +
</body>
 +
</html>
 +
 +
===Usage and Biology===
 +
 +
 +
===Characterization===
 +
====Experimental Design====
 +
<p>To characterize the improved EL222 blue light-inducible system and evaluate the reduction in leakage, we designed a set of experiments involving four distinct plasmid constructs. Each construct either contains or lacks the RAT terminator sequence and the LicV fusion protein gene. These plasmids were co-transformed into <i>E.coli</i> BL21(DE3) cells, and the fluorescence intensity of the reporter gene (sfGFP) was measured over time under blue light or dark conditions.</p>
 +
 +
<p>The experimental group and three control groups were set up as follows:</p>
 +
 +
<p>
 +
①<b>Experimental group (RAT+ LicV+):</b> Contains both the RAT terminator sequence and LicV fusion protein, expected to show minimal leakage in the absence of blue light and induced sfGFP expression under blue light.</p>
 +
<p>
 +
②<b>Control group 1 (RAT+ LicV-):</b> Contains the RAT terminator sequence but lacks LicV. This group is expected to exhibit minimal sfGFP expression under both light and dark conditions due to the absence of LicV activation.</p>
 +
<p>
 +
③<b>Control group 2 (RAT- LicV+):</b> Contains LicV but lacks the RAT terminator sequence. This group may show increased sfGFP expression and potential leakage in the absence of blue light due to the lack of RNA-based regulation.</p>
 +
<p>
 +
④<b>Control group 3 (RAT- LicV-):</b> Lacks both the RAT terminator sequence and LicV. This group is expected to have the highest leakage due to the absence of both regulatory elements.</p>
 +
 +
<p>All four groups were subjected to both blue light exposure and dark conditions during cultivation, leading to a total of eight experimental setups. Bacteria were cultured at 37°C, and samples were taken every two hours over a 16-hour period for fluorescence and OD<sub>600</sub> measurements by PerkinElmer Ensight multimode plate reader.</p>
 +
 +
====Result====
 +
<p>The fluorescence intensity of sfGFP was measured at multiple time points across the 16-hour period under both blue light and dark conditions. Overall, fluorescence levels increased under blue light, especially in groups containing the LicV protein. However, both the experimental group (RAT+ LicV+) and Control Group 2 (RAT- LicV+) exhibited lower fluorescence intensity compared to Control Group 3 (RAT- LicV-) under blue light. This difference is likely due to the metabolic burden imposed by the RAT terminator and LicV fusion protein, which may divert cellular resources and thus reduce sfGFP expression.</p>
 +
 +
<p>In contrast, Control Group 3 (RAT- LicV-) showed the highest fluorescence under blue light, suggesting that the absence of these regulatory elements minimized metabolic strain, leading to greater expression efficiency. Fluorescence levels in all groups remained low in the dark, confirming that the system effectively minimized leakage.</p>
 +
 +
<html lang="zh">
 +
<head>
 +
    <meta charset="UTF-8">
 +
    <meta name="viewport" content="width=device-width, initial-scale=1.0">
 +
    <style>
 +
        .module {
 +
            border: 1px solid #ccc; /* 边框 */
 +
            padding: 20px; /* 内边距 */
 +
            margin: 20px auto; /* 外边距，自动居中 */
 +
            width: 500px; /* 模块宽度 */
 +
            text-align: center; /* 内容居中 */
 +
            box-shadow: 0px 0px 10px rgba(0, 0, 0, 0.1); /* 阴影效果 */
 +
        }
 +
    </style>
 +
</head>
 +
<body>
 +
    <div class="module">
 +
        <img src="" width="400" height="auto" alt="Fluorescence strength of four groups">
 +
        <p><b> Fig. 3 | Fluorescence intensity over time for all groups  </b></p>
 +
    </div>
 +
</body>
 +
</html>
 +
 +
<p>The microscopy images visually confirm the trends observed in the enzyme-linked measurements. Groups with lower fluorescence intensities in the plate reader data (e.g., the experimental group and Control Group 2) also show weaker fluorescence under the microscope, further supporting the hypothesis that the metabolic burden from the regulatory elements affects sfGFP expression. Conversely, Control Group 3 exhibits stronger fluorescence, consistent with the data from the microplate reader.</p>
 +
 +
<html lang="zh">
 +
<head>
 +
    <meta charset="UTF-8">
 +
    <meta name="viewport" content="width=device-width, initial-scale=1.0">
 +
    <style>
 +
        .module {
 +
            border: 1px solid #ccc; /* 边框 */
 +
            padding: 20px; /* 内边距 */
 +
            margin: 20px auto; /* 外边距，自动居中 */
 +
            width: 500px; /* 模块宽度 */
 +
            text-align: center; /* 内容居中 */
 +
            box-shadow: 0px 0px 10px rgba(0, 0, 0, 0.1); /* 阴影效果 */
 +
        }
 +
    </style>
 +
</head>
 +
<body>
 +
    <div class="module">
 +
        <img src="" width="400" height="auto" alt="Fluorescence microscopy images">
 +
        <p><b> Fig. 4 | Fluorescence microscopy images comparing the final time-point samples from different groups </b></p>
 +
    </div>
 +
</body>
 +
</html>
 +
 +
<!-- Add more about the biology of this part here
 +
===Usage and Biology===
 +
 +
<!-- -->
 +
<span class='h3bb'>Sequence and Features</span>
 +
<partinfo>BBa_K5398630 SequenceAndFeatures</partinfo>
 +
 +
 +
<!-- Uncomment this to enable Functional Parameter display
 +
===Functional Parameters===
 +
<partinfo>BBa_K5398630 parameters</partinfo>
 +
<!-- -->

Revision as of 17:04, 27 September 2024

Use LicV fusion protein to improve the leakage of the BBa_K3739064 system

LicV is a fusion protein, which could be activated with blue light. It consists of the N-terminal RNA-binding domain (coantiterminator, CAT) of LicT and Vivid(VVD) which is a small LOV domain-containing protein. When induced by blue light, VVD dimerizes and leads to the conformational changes of LicT, thus stabilizing the LicT dimer and specifically binding a ribonucleic antiterminator (RAT) RNA sequence to prevent the formation of an RNA terminator stem–loop structure.

Introduction

EL222 is a natural photosensitive DNA-binding protein that dimerizes and binds DNA upon blue light exposure. It is composed of a N-terminal light-oxygen-voltage(LOV) domain and a C-terminal helix-turn-helix(HTH) DNA-binding domain characteristic of LuxR-type DNA-binding proteins. EL222 could act as a transcriptional activator in a tunable blue light-inducible promoter system. pBlind, a synthetic blue light-inducible promoter, is formed by replacing the lux box which is a 20-bp inverted repeat from the luxI promoter with the 18-bp EL222 binding protein region. When exposed to blue light, EL222 dimerizes and overlaps the -35 region of the promoter thus recuiting RNAP. But a high leakage level of this blue light-induced system is witnessed. Aiming to lower the leakage, XMU-China 2021 replaced the strong promoter BBa_J23106 with pBlind. Although the leakage issue has improved somewhat, a quantity of reporter genes will still be expressed without blue light.

Original EL222 system

Fig. 1 | EL222 system designed by XMU-China 2021

LicV is a fusion protein, which could be activated with blue light. It consists of the N-terminal RNA-binding domain (coantiterminator, CAT) of LicT and Vivid(VVD) which is a small LOV domain-containing protein. When induced by blue light, VVD dimerizes and leads to the conformational changes of LicT, thus stabilizing the LicT dimer and specifically binding a ribonucleic antiterminator (RAT) RNA sequence to prevent the formation of an RNA terminator stem–loop structure.

Improved EL222 system

Fig. 2 | Improved EL222 system with LicV and RAT

Usage and Biology

Characterization

Experimental Design

To characterize the improved EL222 blue light-inducible system and evaluate the reduction in leakage, we designed a set of experiments involving four distinct plasmid constructs. Each construct either contains or lacks the RAT terminator sequence and the LicV fusion protein gene. These plasmids were co-transformed into E.coli BL21(DE3) cells, and the fluorescence intensity of the reporter gene (sfGFP) was measured over time under blue light or dark conditions.

The experimental group and three control groups were set up as follows:

①Experimental group (RAT+ LicV+): Contains both the RAT terminator sequence and LicV fusion protein, expected to show minimal leakage in the absence of blue light and induced sfGFP expression under blue light.

②Control group 1 (RAT+ LicV-): Contains the RAT terminator sequence but lacks LicV. This group is expected to exhibit minimal sfGFP expression under both light and dark conditions due to the absence of LicV activation.

③Control group 2 (RAT- LicV+): Contains LicV but lacks the RAT terminator sequence. This group may show increased sfGFP expression and potential leakage in the absence of blue light due to the lack of RNA-based regulation.

④Control group 3 (RAT- LicV-): Lacks both the RAT terminator sequence and LicV. This group is expected to have the highest leakage due to the absence of both regulatory elements.

All four groups were subjected to both blue light exposure and dark conditions during cultivation, leading to a total of eight experimental setups. Bacteria were cultured at 37°C, and samples were taken every two hours over a 16-hour period for fluorescence and OD600 measurements by PerkinElmer Ensight multimode plate reader.

Result

The fluorescence intensity of sfGFP was measured at multiple time points across the 16-hour period under both blue light and dark conditions. Overall, fluorescence levels increased under blue light, especially in groups containing the LicV protein. However, both the experimental group (RAT+ LicV+) and Control Group 2 (RAT- LicV+) exhibited lower fluorescence intensity compared to Control Group 3 (RAT- LicV-) under blue light. This difference is likely due to the metabolic burden imposed by the RAT terminator and LicV fusion protein, which may divert cellular resources and thus reduce sfGFP expression.

In contrast, Control Group 3 (RAT- LicV-) showed the highest fluorescence under blue light, suggesting that the absence of these regulatory elements minimized metabolic strain, leading to greater expression efficiency. Fluorescence levels in all groups remained low in the dark, confirming that the system effectively minimized leakage.

Fluorescence strength of four groups

Fig. 3 | Fluorescence intensity over time for all groups

The microscopy images visually confirm the trends observed in the enzyme-linked measurements. Groups with lower fluorescence intensities in the plate reader data (e.g., the experimental group and Control Group 2) also show weaker fluorescence under the microscope, further supporting the hypothesis that the metabolic burden from the regulatory elements affects sfGFP expression. Conversely, Control Group 3 exhibits stronger fluorescence, consistent with the data from the microplate reader.

Fluorescence microscopy images

Fig. 4 | Fluorescence microscopy images comparing the final time-point samples from different groups

Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NheI site found at 7
    Illegal NheI site found at 30
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]