Part:BBa_K1383000
BBa_K1383000 (mCherry- Native RBS)
Usage and Biology
The ribosome binding sites (RBS) of archaea are not well characterized. By creating and characterizing a library of RBS sequences, researchers will be able to express proteins of interest at variable levels of expression in Methanococcus maripaludis. Ribosome binding sites are typically 6-7 base pair sequences on a transcript that is complementary to the 3’ end of the 16S rRNA. After binding of the RBS to the ribosome, translation will be initiated. An RBS with higher affinity for the ribosome will result in higher rate of translation, and inversely, an RBS with lower affinity will result in lower rate of translation.
Characterization
Characterization of the RBS sequences was accomplished using the red fluorescent protein, mCherry as a reporter. Qualitative analysis was evaluated by visualization of the RFP and quantitative analysis was completed through use of a plate reader for reading fluorescence.
Improving the Construct and Characterization of Fluorescent Reporters for use in Methanogens
Last year, the UGA-Georgia team submitted the part BBa_K1138002, named pAW50-mCherry. This construct, designed for use as a fluorescent reporter in methanogens, had a few issues. First, the part was not 100% biobrick compatible due to an internal restriction site in the mCherry gene. The characterization of the part was also inconsistent among samples, and overall unreproducible. To improve upon the previous part, we designed pMEV4-mCherry (BBa_K1383000, figure 1). The primary differences between this construct and the pAW50-mCherry of 2013 is that pMEV4-mCherry does not contain the internal restriction site and the selective resistance gene against puromycin, our antibiotic for use in M. maripaludis, has an independent promoter. Therefore, pMEV4-mCherry is 100% biobrick compatible, and can more reliably function under increased selective pressure. Improvements on characterization are elaborated more below.
The region labeled 'RBS 1-39' in the pMEV4-mCherry vector (figure 1) is the site immediately upstream of the mCherry gene that will be subject to variation. Specifically, we will be mutating the 6 base pairs of the RBS, the 5 of the spacer, and the first base of the start codon. We begin with the 'native' RBS, which is a known functional RBS sequence in methanogens and is typically used for creating synthetic parts. The RBS variants are created by making mutations on only one base at a time for every nucleotide different from the native (figure 2). We designed two additional RBS sequences based off the 16S rRNA data for M. maripaludis, termed theoretical 'perfect' and 'negative' (figure 2, #37 & #38, respectively). These RBS sequences were designed to have the theoretical greatest and worst possible affinities for the 16S ribosome. Figure 3 illustrates the specific sequence for the part described on this page, the 'native' RBS.
Improving the Characterization of Parts which include Fluorescent Reporters in Methanogens
Fluorescence readings in pAW50 (BBa_K1138002) were highly inconsistent and unreproducible. To remedy this, we discovered and addressed two main issues; 1) We removed resazurin from the broth-medium and 2) developed a novel protocol for oxygen exposure to mature the mCherry fluorophore.
Resazurin is an oxidation-reduction indicator which is commonly used in broth-mediums for obligate anaerobes because when resazurin is reduced, for example by oxygen, it turns a pink color which visually indicates to researchers that oxygen accidentally got into a culture. To run samples through a plate reader, we obviously had to take them out of their anaerobic culture and put them on a plate, which led to the reduction of resazurin and the false positives and large inconsistencies in characterization. This was a simple fix, since resazurin isn't required for growth, we made broth-medium that didn't contain resazurin and took extra caution to ensure no oxygen got into any cultures.
Many fluorescent proteins, including mCherry, require oxygen for the full maturation of the fluorophore. Since mCherry is being produced here in an obligate anaerobe, mCherry never had exposure to oxygen. We developed a novel protocol for oxygen exposure for maturation of the mCherry fluorophore produced in M. maripaludis cultures.
In an effort to expand synthetic biology research for Archaea, we have developed protein expression tools to facilitate fluorescence mediated detection of proteins. For our 2014 project we present 3 new BioBrick parts that iGEMers can use readily. All three of our parts are BioBrick compatible. Specifically, we constructed tools consisting of native/ synthetic Methanococcus RBS site(s) upstream of a gene encoding red fluorescent protein-mCherry. Prior to cloning the mCherry gene was codon optimized for expression in Methanoccocus (also, ensuring BioBrick compatibility in the design considerations). The BioBrick part- BBa_K1383000 consists of the native Methanococcus RBS site upstream of the mCherry gene. This fragment was inserted into pSB1C3 plasmid backbone using EcoRI and PstI restriction enzymes.
Sequence and Features
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE WITH RFC[1000]
| n/a | BBa_K1383000 (mCherry- Native RBS) |