All work described on this wiki or on our parts registry pages was done by iGEM Team XMU Software 2013. We managed to finish the whole project, from planning, financing to the complete dry and wet lab work by ourselves. Nevertheless we could not have done all this work without the help, advice and guidance of several people. Therefore, special thanks to the following people:

Team XMU China, the wet lab team of our university, gave us a hand to construction work.

Tina Zhang, the advisor of team XMU China, helped us in experiments, especially in site-specific mutagenesis and PCR.

Prof. Zhiliang Ji, College of Life Science, provided us with valuable guidance in choosing the project.

Prof. Shoufa Han, provided us with many instruments such as ELISA reader to test the fluorescence.

Qiang Kou, the previous team leader of SYSU-Software team, gives us lots of help.

Wenjun Rao, a shy boy from XMU Software College, build the beautiful interfaces for Brick Worker.

Abstract

Promoter-decoder is part of our software designed to analyze and evaluate promoters. The software use PWM method to calculate the similarity between promoter sequences and the position frequency matrix of transcription factor binding sites (TFBS) to locate the TFBS as well as to predict the relative strength of the promoter.

Promoter-Decoder enables the users to figure out promoter types, predict promoter strength, change it by mutating the key sites and even change the property of certain promoter by adding new TFBS to the promoter sequence.

Background

Sigma Factors

Bacteria encode several thousands of different proteins, which are necessary for normal cell functions or for adaptation to environmental changes. These proteins are not required at the same time or in the same amount. Regulation of gene expression therefore enables the cell to control the production of proteins needed for its life cycle or for adaptation to extracellular changes. This regulation in turn makes it possible for the bacterium to adequately adapt to rapid changes in the environment. The various steps during transcription and translation are therefore subject to different regulatory mechanisms. The most prominent step in gene regulation is the initiation of transcription in which the DNA-dependent RNA polymerase (RNAP) is the key enzyme. The RNAP or the RNAP core enzyme is the catalytic machinery for the synthesis of RNA from a DNA template. However, RNAP cannot initiate transcription by itself. Initiation of transcription requires an additional polypeptide known as a sigma-factor. Sigma-factors are a family of relatively small proteins that can associate in a reversible way with the RNAP core enzyme. Together, the sigma-factor and the RNAP core enzyme form an initiation-specific enzyme, the RNAP holoenzyme.

The sigma-factor directs RNA polymerase to a specific class of promoter sequences. Most bacterial species synthesize several different sigma-factors that recognize different consensus sequences. This variety in sigma-factors provides bacteria with the opportunity to maintain basal gene expression as well as for regulation of gene expression in response to altered environmental or developmental signals.

The frequency at which the RNAP holoenzyme initiates transcription, also known as the strength of a promoter, is influenced by the promoter sequence and the conformation of the DNA in the promoter region. The sigma-factors recognize two conserved sequences in the promoter region, known as the promoter consensus sequence. Sigma-factors or fragments of sigma-factors bind specifically to promoter DNA sequence and by specific base pair and amino acid substitutions in the promoter consensus sequences or sigma factors. Most bacterial species synthesize several different sigma-factors which direct the RNAP holoenzyme to distinct classes of promoters with a different consensus sequence. This variety in sigma-factors provides the bacterium with the opportunity to maintain basal gene expression as well as for regulation of gene expression in response to specific environmental stimuli.

The identification of bacterial promoters is an essential step in the elucidation of gene regulation. As a general rule, the more complex the life-cycle and environmental niche of a bacterium, the greater the number of sigma factors with corresponding promoter types. Typically however, the most common promoter type is that which regulates the housekeeping genes and the corresponding major sigma-factor is shared by all bacteria (sigma 70 in the well studied Escherichia coli, and its homologues in other species). The binding site for the sigma70-family of promoters is defined by two consensus hexamers, TTGACA and TATAAT, located at approximately −35 and −10, respectively relative to the transcript start site (TSS) and spaced 15–21 base pairs (bp) apart2. RNA polymerase core enzyme associates with the major sigma-factor to form the holoenzyme which in turn binds to its cognate promoters to initiate transcription.

Figure 2 The RNA polymerase Figure 3 Consensus sequence of sigma 70 factor

In prokaryotes, the minimum requirement for RNA polymerase binding is recognition of the promoter by the sigma factor. In general, prokaryotic RNA polymerases can interchange a number of sigma factors which bind and initiate different groups of genes³.

Transcription Factors

Sigma factors are essential for the transcription initiation in Escherichia coli. In addition, promoter strengths are not determined purely by the binding of the sigma factor. other transcription factors can bind specific sequences surrounding or overlapping the promoter to either activate or repress transcription⁴. The mechanism is Transcriptional activators and repressors contribute to and detract from the accessibility of DNA by the RNA polymerase. These transcription-regulating nuclear proteins bind to specific binding sites in the regulatory regions (e.g. promoters, enhancers) of the genes thus providing their activation or repression.

Computational methods of predicting TF binding sites in DNA are very important for understanding the molecular mechanisms of gene regulation.

The binding sites of the same transcription factor show a significant sequence conservation, which is often summarized as a short (5–20 bases long) common pattern called a transcription factor binding site (TFBS) or binding consensus. Our software aims to figure out the possible TFBS in promoters and precisely locate the TFBS so that the user may know the exact sites that play a role in regulating the transcription.

In prokaryotes (lower organisms without nuclei), there are fewer TFs, their motifs tend to be relatively long and the strength of regulation for a particular gene often depends on how closely a particular site matches the consensus for the motif. The more mismatches to the consensus in a binding site, the less often the TF will bind and therefore the less control it will exert on the target gene. So our software will calculate the similarity between the possible TFBS in the promoter and the standard motifs so the user will know to which extent the transcription factor will control the promoter transcription

Primer Design

To facilitate the design of PCR primers of various promoters, we've developed an additional function, namely, primer design in this part og our program. After inputting the promoter sequence, the software will figure out the most suitable primers based on the theory of Thomas K¨ampke1, Markus Kieninger, and Michael Mecklenburg.⁵

Data Source

RegulonDB

Genes and operons that are under control of the same TF are members of that TF's regulon. Although methods for the prediction of regulons have been substantially improved, they are still far from perfect.

Comparative genomics tools can be used to predict regulons in bacterial genomes but the procedure can lead to incorrect regulon calling. Despite this drawback, several regulon databases are available that are based on comparative genomics methods and lack experimental evidence.

Probably the extended and accurate databases of regulons for E.coli are RegulonDB which provides the data source for our program.

Algorithm

Experimental results show that these are the strongest promoters that have been characterized in vitro so far and confirm the hypothesis that the consensus promoter sequence is "best." To calculate the similarity between the promoter sequence and the best sequence, we implement the PWM method ⁶in our program..

PWM (Position Weight Matrix)

Molecular techniques for the identification of promoters are both costly and time consuming, hence in silico methods are an attractive and well explored alternative. The most common in silico method to identify _70 promoters uses position weight matrices (PWMs) and depends on the relative conservation of the transcription factor binding site (TFBS, or motifs ).

The algorithm can be divided into two parts regarding to the difference between the motifs of sigma factors and other transcription factors.

Part 1: the recognition of other transcription factors⁷

Other transcription factors are proteins that can bind to a specific DNA sequence (motifs) and regulate the promoter's transcription. To recognize these possible motifs in a given promoter sequence, we calculate the Matrix Similarity Score (MSS) of every possible sites in the promoter sequence using the position frequency matrix of 86 transcription factors published by RegulonDB. The algorithm reports only those matches of a matrix that have got MSS higher than the settled threshold. And MSS for a subsequence x of the length L is calculated in following steps:

f_i,Bi, frequency of nucleotide B to occur at the position i of the matrix (B ∈{A, T, G, C})

fi^min, frequency of the nucleotide which is rarest in position i in the matrix

fi^max, highest frequency in position i.

The information vector

describes the conservation of the positions i in a matrix.Multiplication of the frequencies with the information vector leads to a higher acceptance of mismatches in less conserved regions, whereas mismatches in highly conserved regions are very much discouraged. This leads to a better performance in recognition of TF binding sites if compared with methods that do not use the information vector.

To determine the best threshold of the motif finding algorithm, we test various threshold values and analyze the true negative and false positive rate of each threshold value. The ideal threshold is supposed to have both the least true negative and false positive rates.

The picture above shows part of our test results and to keep both the true negative and false positive rates at a reasonable level, we adopt 3 threshold values, namely, low (0.5977) , median (0.0778) and high (0.85), with a true negative rate at 0.1, 0.5, and 0.7 respectively. And for more flexibility, we also allow the users to set their own thresholds.

Part2: the recognition of sigma factor motif and the evaluation of relative promoter strength.

In the case of sigma 70 factors, the motifs are the −35 and −10 hexamers. enclosing a spacer of length 15–19 bp.

Given a known or predicted TSS location, the corresponding predictions for the −10 and −35 hexamers are located using a combination of two PWMs which are derived from literatures. For any known or putative TSS, the −35 and −10 hexamers are located upstream of the TSS by searching for the highest combination of PWM scores, subject to two constraints:

1. That the spacer length (the number of base pairs between the −35 hexamer and the −10 hexamer) should lie in the range {15–20};

2. The total MSS (our results are the sum of the scores for the −10 and −35 hexamers and therefore lie in the interval [0,2], with a score of 2 corresponding to the joint consensus TTGACA (−35) and TATAAT (−10).

Score(Promoter)=score(-10 box)+score(-35 box)+score(spacer between-10 & -35 boxes)

And the score of spacer length is calculated by algorithms propozed by Ryan K. Shultzaberger.el.in Escherichia coli sigma70 promoters². But due to a lack of experimental data of promoter strength with both different motifs and spacer length, the weight of the total MSS and the spacer score is very roughly determined with few experimental data available. Currently our weight is determined with the promoter strength data in a literature⁸ to best fit the the promoter score with promoter strength. Now the relative weight between the total MSS of the two motifs and the spacer score is 0.29:0.71.

In prokaryotes, the strength of sigma factor regulation for a particular gene often depends on how closely a particular site matches the consensus for the motif. The more mismatches to the consensus in a binding site, the less often the sigma factor will bind and therefore the less strength the promoter will have. Experiments have confirmed the hypothesis that the consensus promoter sequence is “best”. We set the best promoter strength to 100% and calculate the relative strength of a given promoter by the Score (promoter)

Primer design

A primer pair (p, q) is assigned the scoring vector

sc(p, q) = (|p|, |q|,GC(p),GC(q), Tm(p), Tm(q), sa(p),sa(q), sea(p), sea(q), pa(p, q), pea(p, q))^T ∈ R¹²

All primers are designed to have ideal values of length,GC content, and melting temperature which are specified externally by the designer of the hybridization experiment. These ideal values are to be specified for forward and reverse primers. The ideal score vector or reference vector for the primer pair is

sc_ideal =(length_f , length_r,GC_f ,GC_r , T_m,f ,T_m,r , 0, 0, 0, 0, 0, 0)^T.

All ideal annealing values are set to zero and typically

T_mf= T_m,ras well as GC_f = GC_r . The final assessment of a primer pair (p, q) can be its deviation from the reference in terms of the l1-distance

Here, we employ a weighted distance

with weights given in the following table.

The formulas for calculating the variations above are provided in Efficient primer design algorithms⁵.

Results

Sigma factors recognition

Our program has a correctness rate of 56% in recognition various types of sigma factors. We ran our program with 100 various promoters sequences whose types have already been confirmed experimentally. And we’ve recognized 56 of them correctly. Specifically, as for sigma 70 promoters, which are the most prevalent, the recogtion correctness rate has reached 92%. The results are showed below.

Link to the page of results

TFBS Location

We then test the reliability of our software regarding TFBS location and results show that the correct site prediction rate is 64%.We used the sigma70 promoter sequence with annotated -35 and -10 region provided by RegulonDB to test the correct prediction rate of the binding site of a specific transcription. We input 89 sigma70 promoter sequences and ran our program to precisely locate the sigma factor binding site.

The test results are as follows. The numbers represent the site of actual-35 motif, the actual spacer length, the predicted site and predicted spacer length respectively.

Link to the page of reaults

Promoter strength correlation & experiments

To testify our prediction of promoter strength, our team has done a considerable amount of lab work. First, we located the -10 region of the pBAD promoter (BBa _K206000) and accordingly mutated the -10 region into BBa _K1070002, BBa _K1070003, the sequences of these promoters are given bellow (-10 regions are highlighted):

Pba dSt rong (BBa _K206000)：a c a t t g a t t a t t t g c a c g g c g t c a c a c t t t g c t a t g c c a t a g c a a g a t a g t c c a t a a g a t t a g c g g a t c c t a c c t g a c g c t t t t t a t c g c a a c t c t c t a c t g t t t c t c c a t a c c g t t t t t t t g g g c t a g c

BBa _K1070002：a c a t t g a t t a t t t g c a c g g c g t c a c a c t t t g c t a t g c c a t a g c a a t a t a g t c c a t a a g a t t a g c g g a t c c t a c c t g a c g c t t t t t a t c g c a a c t c t c t a c t g t t t c t c c a t a c c g t t t t t t t g g g c t a g c

BBa _K1070003：a c a t t g a t t a t t t g c a c g g c g t c a c a c t t t g c t a t g c c a t a g c a a g a t a a t c c a t a a g a t t a g c g g a t c c t a c c t g a c g c t t t t t a t c g c a a c t c t c t a c t g t t t c t c c a t a c c g t t t t t t t g g g c t a g c

Subsequently, we measured the fluorescence intensity of these promoters and relate it to the actual promoter strength.the experimental results are shown in Figure 9.

Than we fit the actual strength and the predicted strength, as can be seen in figure 9, the coefficient of determination is 0.8924.

Future work

Apply our algorithms to more species. Now Pro-decoder is designed expressly for prediction and evaluation of E.coli promoters, in the near future we’ll study the transcription regulation mechanism of other species and try to apply our algorithms to an extended range of species.

Enhance promoter strength prediction accuracy. Because our experimental data is so limited, the weight of the spacer length and the motif similarity is roughly determined, which lead to a weak correlation between the promoter strength. In the future we hope to obtain more experimental data with regard to the effect of spacer length and motif similarity having on promoter strength so we can revise the weight coefficient of the two factors and get more reliable results.

The next version of this part of our program will be able to analyze not only the promoters of E.coli, but other species such as Bacillus subtilis, we’ll integrate the transcription factor binding site data of more species into our database and use PWM algorithm to predict the TFBS in the promoters.

References

Abstract

RBS-decoder is a software tool for evaluating the relative strength of RBS sequence. This program use the same method—PWM to calculate the similarity between RBS sequence and the position frequency matrix of SD sequence and transform the similarity to the relative strength of an RBS sequence.

Background

Translational efficiency in Escherichia coli is generally determined at the stage of initiation. There are several principal mRNA sequence elements which can affect the kinetics of ternary initiation complex formation (30 S-mRNA-fMet-tRNA): the initiation codon, the Shine-Dalgarno (SD) sequence, the spacing between those two elements, and other factors.

Introduction

How do baterial Ribosome Binding Sites work?

The bacterial ribosome binds to particular sequences on an mRNA, primarily the SD sequence and the start codon (ATG). The SD sequence base-pairs with an RNA molecule that forms part of the bacterial ribosome (the 16s rRNA), while the start codon base-pairs with the initiator tRNA which is bound to the ribosome. In addition to SD sequence and the start codon being important, these two sequences need to be positioned approximately 6-7 nucleotides apart so they can both make contact with the appropriate parts of the ribosome complex1.

The Shine-Dalgarno Sequence

The RBS sequence logo representing the sequences of 149 RBS from E. coli. The height of each letter represents the frequency of the base at that location. From Tom Schneider, "A Gallery of Sequence Logos".

The end of the 16s rRNA that is free to bind with the mRNA includes the sequence 5′–ACCUCC–3′. The complementary sequence, 5′–GGAGGU–3′, named the Shine-Dalgarno sequence, can be found in whole or in part in many bacterial mRNA. Very roughly speaking, ribosome binding sites with purine-rich sequences (A's and G's close to the Shine-Dalgarno sequence will lead to high rates of translation initiation whereas sequences that are very different from the Shine-Dalgarno sequence will lead to low or negligible translation rates. The sequence is named after the researchers who discovered the high frequency of the sequence upstream of bacterial coding sequences . You can see how common the sequence is by looking at the RBS sequence logo on the right (where the height of a letter indicates the frequency of the letter at that location).

Algorithms

As we know, the RBS strength is greatly influenced by the SD sequence, where the 16s RNA of the ribosome binds to, so the strength can be determined by the free binding energy between the SD sequence and the 16s RNA. So we designed a program calculating the free binding energy but the results show that the correlation between the free energy and the strength of RBS is rather weak (R2=0.5517). So we decide to find other algorithms for better accuracy.

Inspired by the strength prediction algorithms used in promoter part, in which the similarity to the sigma factors' PWM is interlocking with the binding affinity between the protein and DNA sequence. We obtained the Position Frequency Matrix of SD sequence of E.coli and use the PMW method (illustrated in detail in the promoter part) to calculate the similarity between the RBS sequence and the Position frequency sequence, what is different from the promoter is that, the spacer length between the SD sequence and the startcodon and the start codon itself both act as constraints in locating the SD sequence, which is confined to 3-16 bp and ATG/TTG/GTG. And similar to the prediction of promoter strength, the spacer length between the SD sequence also contribute to the RBS strength, the optimal spacer length is 7 bp, and the spacer score is calculated using the same algorithm applied in the promoter part. The weight of the influence of the spacer on strength is derived from the algorithm to predict the promoter strength, in which the weight of the total MSS and the spacer is 0.29:0.71, and since in promoter the total MSS is the sum of two motifs while the SD sequence is only one motif, the weight between the MSS(SD sequence) and the spacer is 0.29:0.355.

Nucleotide frequencies for the RBS model

	1	2	3	4	5
T	0.161	0.050	0.012	0.071	0.115
C	0.077	0.037	0.012	0.025	0.046
A	0.681	0.105	0.105	0.861	0.164
G	0.077	0.808	0.960	0.043	0.659

Results

We use the RBS sequence listed on the iGEM registry with experimentally determined relative strength⁴, and the correlation between the RBS strength predicted by our software and the actual relative strength is strong, with a determination coefficient value 0.8039.

Future work

Due to scarcity of experimental data, the relative weight of the SD sequence and the spacer length used currently is roughly determined which may undermine the accuracy of RBS strength prediction. For further improvement of our program, we'll try to obtain more reliable experimental data to accurately determine the weight used in our algorithm and hopefully elevate the accuracy of RBS-decoder.

In the next version of RBS-decoder, the secondary structure of the RBS sequence will be shown on the software and we'll also include the other species' SD sequence data in order to analyze predict the strength of RBS.

Reference

Background

Gene expression in both prokaryotes and eukaryotes is frequently controlled at the level of transcription. This process can be represented as a cycle consisting of four major steps: (1) promoter binding; (2) RNA chain initiation; (3) RNA chain elongation; and (4) termination. Since regulatory controls are exerted at each step, an understanding of the mechanism of each step is of general importance in understanding gene expression.

In the promoter part of our program, we've discussed the mechanism of promoter binding step and how it affects the transcription level. To complete our biobrick evaluation program and to better understanding of transcription process, we integrated the software developed by 2012 iGEM team SUSTC-Shenzhen-B to realize the prediction of transcription termination efficiency.

Introduction

Termination, the last step of the transcription cycle, occurs when the RNA polymerase releases the RNA transcript and dissociates from the DNA template. It is important that transcription is imperfectly terminated at some terminator so that the ratio of the amount of the mRNA transcribed from upstream and that from downstream of the terminator is controlled. This regulation is quantified by the termination efficiency (%T),

Two mechanisms of transcription termination and two classes of termination signals have been described in bacteria: rho-dependent and rho-independent.

Rho-independent (also known as intrinsic) terminators are sequence motifs found in many prokaryotes that cause the transcription of DNA to RNA to stop. These termination signals typically consist of a short, often GC-rich hairpin followed by a sequence enriched in thymine residues.

The conventional model of transcriptional termination is that the stem loop causes RNA polymerase to pause and transcription of the poly-A tail causes the RNA: DNA duplex to unwind and dissociate from RNA polymerase.

Algorithm

In 2011, iGEM team SUSTC-Shenzhen-B developed a software tool TTEC to predict terminator efficiency. It takes DNA sequences as input and returns the terminator efficiency value.

In the algorithm, it takes 3 steps to calculate the terminator efficiency:

1. Use RNA folding algorithm to predict the secondary structure of terminator and and recognize A tail, stemloop and T tail.

2. From the secondary structure, we calculate the free energy of stem loop, and generate a score by considering stem loop free energy and T tail

3. From the score, we predict the terminator efficiency based on the score-terminator equation.

The prediction of secondary and recognition of A tail, stemloop and T tail are achieved by Kings ford scoring system.

Kingsford Scoring System

In 2007, Carleton L Kingsford et al described TransTermHP1, a new computational method to rapidly and accurately detect Rho-independent transcription terminators.

They put forward an algorithm to predict Rho-independent terminators.The first 15 bases of the potential tail sequence are scored using a function:

where

for n=1...15 and =1.

The energy of potential hairpin configurations adjacent to a reference position can be found efficiently with a dynamic programming algorithm. The table entry hairpin_score[i,j] gives the cost of the best hairpin structure for which the base of the 5' stem is at nucleotide position i and the base of the 3' stem is at position j. The entry hairpin_score[i,j] can be computed recursively as follows:

The function energy(i,j) gives the cost of pairing the nucleotide at i with that at j, and loop_pen(n) gives the cost of a hairpin loop of length n. The hairpin's loop is forced to have a length between 3 and 13 nt, inclusive, by setting loop_pen(n) to a large constant for any n outside that range. The constant 'gap' gives the cost of not pairing a base with some base on the opposite stem and thus introducing a gap on one side of the hairpin stem.

Table 1

Parameters used to evaluate hairpins

Pairing Energy

G-C -2.3

A-T -0.9

G-T 1.3

Mismatch 3.5

Gap 6.0

Loop_pen(n) 1•(n - 2)

Parameters used to evaluate the energy of a potential hairpin where n is the length of the hairpin loop

The D score is calculated by Carafa Scoring System

Carafa Scoring System

Scoring System 2 is based on the model created by d'Aubenton Carafa 2 .The score of terminator consists of two parts, the free energy of stemloop and the score of 15 nt poly T tail. The free energy of stemloop is calculated using Loop Dependent Energy Rules 3. The minimization of the free energy also determined the secondary structure of the stemloop. T tail score is calculated by the formula given by d' Aubenton Carafa.

Detailed Calculation of Score

1. Some definitions3

i. Closing Base Pair

For an RNA sequence, we number it from 5' to 3' . If i < j and nucleotides ri and rj form a base pair,we denote it by i.j. We call base ri' or base pair i'.j' is accessible from i.j if i <i' ( <j' ) <j and if there is no other base pair k.l so that i <k <i' ( <j' ) <l <j. We denote the collection of base and base pair accessible from i.j by L(i,j). Then i.j is the closing base pair. Here “L” means loop.

ii. n-loop

If the loop contain n – 1 base pairs, we denote it by n-loop. (Because there is a closing base pair, so we denote it by n-loop even though the closing base pair is not included in the loop.)

Here we can divide loops which may be formed in the terminator secondary structure into two kinds.

1-loop : Hairpin loop(size of loop shouldn't be smaller than 3)

2-loop : Interior Loop(right strand size and left strand size are both bigger than 0.)

Buldge(Size of one strand is bigger than 0 and that of another strand is 0.)Stack(size of the loop is 0.)

2. Calculation of the Minimum Free Energy Change of Stemloop Formation4 Assume i.j is the closing base pair of the loop

G（i,j）= min { GH ( i , j ) , GS( i , j ) + G ( i + 1 , j – 1 ) , GBI( i , j ) } ;

GBI ( i , j ) = min{ gbi( i , j , k , l ) + G( k , l ) } for all 0 < k – i + l – j - 2 < max_size

G(i,j) is the minimum free energy change of stemloop formation. GH is the free energy change to form a hairpin loop. GS is the free energy change to form a stack. GBI is to calculate the minimum free energy change of structure containing 2-loop. gbi(i,j,k,l) is the free energy change to form 2-loop.

3.Calculation of T Tail Score

Here we consider 15 nucleotide in the downstream of stemloop. T tail score nT is calculated as follows :

In our program, if the length of the T tail( n ) is less than 15, we will only consider n nucleotides. If TL is more than 15, we will only consider 15 nucleotides.

4.Calculation of Score

Score = nT * 18.16 + deltaG / LH * 96.59 – 116.87

Here nT is T tail score. deltaG is the minimum free energy change of stemloop formation. LH is the length of stemloop^5.6

References

Abstract

Our team mainly focuses on programming the software by two methods using genetic algorithm, evaluating both optimization of single codon and codon pair and hence determining the fittest optimized sequence for expression in heterologous host cell.

Apart from the optimization, we have two additional functions. One is the statistics analysis, which provides the numbers and the proportion of the codon in the original and optimized sequence, making the optimization easier to understand. The other is the prediction of the protein folding rate. The purpose of the prediction is to seek the law of the folding rate in general, computing a relatively accurate folding rate value of the optimized sequence for the users.

Background

Synonymous codons and the efficiency

Except methionine and tryptophan, all amino acids can be encoded by two to six synonymous codons, resulting from the degeneracy of the genetic code.1 However, unequal utilization of the synonymous condons leads to the phenomenon of codon usage bias, which is mainly due to natural selection, mutation and genetic drift.2 According to related studies, codon usage bias has certain connection with gene expression level. 3The larger the value of codon usage bias is, the higher gene expression will be. So the problem, how to substitute the synonymous codons aimed at raising the efficiency of gene expression and thus increasing the production of recombination protein in heterologous host cell, is expected to be addressed.

Protein folding rate

Protein is an important class of biological macromolecules. It is the main bearer of life activities and occupies a special position in vivo. Each protein has its own unique amino acid composition and sequence. Only when the amino acid chain is folded into the correct three-dimensional structure, will the protein have normal biological functions. Misfolded ones will not only lose its biological function but also even cause diseases such as mad cow disease, Alzheimer's syndrome, etc. The protein folding problem, an important biological question that the central dogma of molecular biology has not solved yet, has been listed as an important topic in twenty-first century. The folding mechanism of the protein is a challenging task, one of which is to determine factor influencing the folding rate. Although the answer can be found in a variety of biological experiments, such as various spectroscopy, mass spectrometry and nuclear magnetic resonance, these methods are time-consuming and costly. With the development of physics, mathematics, especially the progress of computer technology, how to apply a fast and accurate calculation method to predict protein folding rate attracts more and more attention.⁴

Introduction

Balance with single codon and codon pair

Individual codon usage optimization has been attached importance to, taking Codon optimizer⁵, Gene Designer⁶, OPTIMIZER⁷ for example. Subsequently, people found the effect of gene expression optimization cannot be perfect just by single codon optimization. Codon pair, namely the pair of k-th and (k+1)-th codons from the 5’ to 3’ end, is another crucial factor. Due to potential tRNA-tRNA steric interaction within the ribosomes⁸, the usage of rare condon pairs, which correlate with translation elongation, decrease protein translation rates⁹. Optimization of individual codon has an influence on the corresponding codon pair resulting in maybe-not-the-best codon pair optimization. In the same way, optimizing codon pair merely contributes to maybe-not- the-best single codon optimization. Therefore, it is a challenging way for us to apply a method considering and weighing the effects of single codon and codon pair optimization and thus make the whole best.

Our team focuses on evaluating both optimization of single codon and codon pair and thus selecting the best sequence for expression in heterologous host cell.

Host Cell

Considering E. coli and S. cerevisiae are the ideal hosts for recombinant proteinexpression, and Gram-positive bacterium L. lactis and methylotrophic yeast P. pastoris are also promising candidates for expressing recombinant proteins¹⁰, we attached importance to selecting these four kinds of bacterium as host cell to optimize the sequence.

Method of prediction

In recent years, many researchers have made great efforts to explore the determinants of the folding rate, and various forecasting methods have been proposed. The existed prediction methods can be roughly divided into three categories11-12. The first one is based on the tertiary structure13-19. However, it takes lots of molecular experiments, expensive and in long period, to acquire the information of the tertiary structure, which fails to meet the demand of rapid prediction. The second category is based on the secondary structure20-24. This kind of method requires information of the secondary structure, similarly obtained by molecular experiments, or from the primary sequence prediction, but it will be limited by accuracy of the secondary structure prediction method. The last one is based on the primary structure25-34, which predicts the folding rate from amino acid sequences without most structure information.4And our prediction of the protein folding rate focuses on the last method.

Algorithm

Part I—method I: MOCO³⁵

Basic Table

Based on the table below, we calculate function of single codon (ICU) , function of codon pair (CCO) and the function of multi-objective codon optimization (MOCO). MOCO aims at make the optimization of whole best by calculating the relative effect of ICU and CCO.

Amino acid abbreviation and synonymous codons.¹¹

Amino Acid	Abbreviation	Synonymous Codon(s)
Methionine	M	AUG
Tryptophan	W	UGG
Cysteine	C	UGC, UGU
Aspartate	D	GAC, GAU
Glutamate	E	GAA, GAG
Phenylalanine	F	UUC, UUU
Histidine	H	CAC, CAU
Lysine	K	AAA, AAG
Asparagine	N	AAC, AAU
Glutamine	Q	CAA, CAG
Tyrosine	Y	UAC, UAU
Isoleucine	I	AUA, AUC, AUU
Alanine	A	GCA, GCC, GCG, GCU
Glycine	G	GGA, GGC, GGG, GGU
Proline	P	CCA, CCC, CCG, CCU
Threonine	T	ACA, ACC, ACG, ACU
Valine	V	GUA, GUC, GUG, GUU
Leucine	L	CUA, CUC, CUG, CUU, UUA, UUG
Arginine	R	AGA, AGG, CGA, CGC, CGG, CGU
Serine	S	AGC, AGU, UCA, UCG, UCC, UCU
(Stop)	*	UAA,UAG,UGA

Calculation of ICU

max

s.t.

Calculation of CC

max

s.t.

In the function,

Kronecker Delta function

Calculation of MOCO

The MOCO calculation is as follows (NSGA-II algorithm applied):

1. Randomly initialize a population of coding sequences for target protein.

2. Evaluate ICU and CC fitness of each sequence in the population.

3. Group the sequences into nondominated sets and rank the sets.

4. Check termination criterion.

5. If termination criterion is not satisfied, select the “fittest” sequences (top 50% of the population) as the parents for creation of offsprings via recombination and mutation.

6. Combine the parents and offsprings to form a new population.

7. Repeat steps 2 to 5 until termination criterion is satisfied.

The identification and ranking of nondominated sets in step 3 is performed via pair-wise comparison of the sequences' ICU and CC fitness. For a given pair of sequences with fitness values expressed as and , the domination status can be evaluated as follows:

• If > and >= , sequence 1 dominates sequence 2.

• If >= and > , sequence 1 dominates sequence 2.

• If < and <= , sequence 2 dominates sequence 1.

• If <= and < , sequence 2 dominates sequence 1.

The process is showed in the figure below:

Multi-objective codon optimization solution. The optimal solutions generated by MOCO lies on the pareto front (region in yellow).¹¹

At the first, we decided on this method and we also programmed the software by MOCO method. However, we found two problems. One is that the calculation of ICU and CC fitness is only based on mathematical rationality, and lacks of enough experimental data to prove the result. And the other, we would like to find a fitness function, which weighs both the two aspects as a whole. Therefore, in order to tackle with the problem, we chose the method II below as the one recommended.

Part II—method II: Fitness³⁶

Fitness function：

In the function,

cpi is a value larger than zero, ranging from 10^-4 to 0.5，fit_cp(g) is the fitness function of the codon pair，fit_sc(g) is the fitness function of the single codon，w((c(k)，c(k+1)) is the weight of codon pairs in sequence g，|g| is the length of encoding sequence，c(k) is k-th codon in the sequence， is the target ratio of k-th codon, is the actual ratio of k-th codon in the sequence，the best value of cpi is 0.2 in the software.

In the function, the target ratio of k-th codon can be approximated by the equation below:

In the function, weight can be calculated by the equation below:

stands for the ratio of single codon c_kin the complete genome'is the number of pair (c_i,c_j) in high-expression genes，and high-expression genes are genes whose copy numbers of mRNA can be detected at least 20 per cell.

syn(c_k)stands for the synonymous codon set related to c_k,equals to the number of amino acid encoded by c_i in the whole protein set.

By this method, there are enough experimental data to prove the sequence optimized works. Xylose isomerase in Bacillus stearothermophilus, Xylose isomerase in Streptomyces olivochromogenes and L-arabinose isomerase in Thermoanaerobacter mathranii all, the optimized ones, were highly expressed in Bacillus subtilis. In addition, the activity of the optimized Aspergillusniger fungal amylase was enhanced to 400% compared with the original sequence in A. niger.³⁶

Part III—Prediction of protein folding rate

In order to illustrate protein folding rate quantitatively, we determine the folding rate of 60 kinds of proteins as an experimental data set from literature and database37, and information of the sequence comes from PBD and NCBI.

protein	Logarithm of the folding rate Ln(kf)	protein	Logarithm of the folding rate Ln(kf)	protein	Logarithm of the folding rate Ln(kf)
2PDD	9.8	1FKB	1.5	1RA9	-2.5
2ABD	6.6	2CI2	3.9	1QOP	-6.9
256B	12.2	1URN	5.8	1PHP	2.3
1IMQ	7.3	1APS	-1.5	1PHP	-3.5
1LMB	8.5	1RIS	5.9	1BNI	2.6
1WIT	0.4	1POH	2.7	2LZM	4.1
1TEN	1.1	1DIV	6.1	1UBQ	5.9
1SHG	1.4	2VIK	6.8	1SCE	4.2
1SRL	4	1A6N	1.1	1YCC	9.62
1PNJ	-1.1	1CEI	5.8	1VII	11.52
1SHF	4.5	2CRO	3.7	1NYF	4.54
1PSF	3.2	2A5E	3.5	2AIT	4.2
1CSP	7	1IFC	3.4	1PIN	9.44
1C9O	7.2	1EAL	1.3	1C8C	6.91
1G6P	6.3	1OPA	1.4	1BRS	3.4
1MJC	5.3	1CBI	-3.2	1UBQ	5.9
1LOP	6.6	1QOP	-2.5	3CHY	1
1C8C	7	1BRS	3.4	1BIN	2.6
1HZ6	4.1	3CHY	1	1SCE	4.2
1PGB	6	2RN2	0.1	1GXT	4.38

In order that the characteristic factors of the folding rate can be extracted from protein sequences, we introduced the Chou's pseudo amino acid composition concept³⁸. According to the pseudo amino acid composition principle, the position information of protein sequences can be, to some extent, reflected by a group of serial correlation factors θ₁，θ₂ ，θ₃……，θ_n ,which is defined as follows:

in the function, θ₁ is called the first-tier correlation factor that reflects the sequence order correlation between all the most contiguous residues along a protein chain (Fig. 1a), θ₂ the second-tier correlation factor that reflects the sequence order correlation between all the second most contiguous residues (Fig.1b), θ₃ the third-tier correlation factor that reflects the sequence order correlation between all the 3rd most contiguous residues (Fig.1c), and so forth³⁸.

the correlation function is given by⁴:

where H1(Ri), H2(Ri), and M(Ri) are, respectively, the hydrophobicity value. Studies have shown that λ=10 will be the best predictor³⁹. But there will be a large amount of calculation considering all possible situations—the 30 factors. We should select factors that can obtain the best prediction accuracy in least calculation. For that reason, we drew lessons from the literature⁴ by using the method of Monte Carlo simulation and then 14 optimal characteristic factor were obtained. Other studies have indicated that the logarithm of the sequence length has a good correlation with folding rate, so Ln (L) will be the fifteenth factors. We apply SPSS software to calculate the coefficient of 15 factor by multivariate linear regression, and this will be the forecast formula of the rate of protein folding. We compared the experimental data and the predicted data and the results are as follows:

Through the test, our software succeeded in showing a relatively accurate folding rate value.

Future work

1. Shortening the computing time of the software.

2. Expanding the range of the host cells.

3. Improving bacterium's resistance to toxic molecule.

4. Advancing existed paths of synthetic biology by the method.

5. Designing new paths of synthetic biology by the method.

6. Increasing the output of recombinant protein.

7. Predicting the expression of heterologous gene in a new host cell.

8. considering more factors such as spiral structure in folding which influence the folding rate and thereby abtaining more accurate prediction rate.

9. providing a set of software tools for protein folding, especially in molecular dynamics simulation of protein folding.

References

Basic Safety Question for iGEM 2013

1. List and describe all new or modified coding regions you will be using in your project. (If you use parts from the 2013 iGEM Distribution without modifying them, you do not need to list those parts.)

2. Highest Risk Group Listed

1

3. Please describe the chassis organism(s) you will be using for this project. If you will be using more than one chassis organism, provide information on each of them:

4. Do the biological materials used in your lab work pose any of the following risks? Please describe.

a. Risks to the safety and health of team members or others working in the lab?

No. According to the Final Risk Assessment of the U.S. Environmental Protection Agency (EPA) (1997), Escherichia coli K-12 are not likely to pose any risk to human or animal health, to plants or to other microorganisms. In addition,We will use gloves and eye protected glasses during the experiments.

b. Risks to the safety and health of the general public , if released by design or by accident?

No. Escherichia coli K-12 are not likely to pose any risk to human or animal health, to plants or to other microorganisms. Although strains we use in our lab work have antibiotic genes, but they can still be killed by other common antibiotics.We only use E. coli and we will have disinfection after the experiment.

c. Risks to the environment, if released by design or by accident?

No. Since Escherichia coli K-12 are ubiquitous in the environment, they won't endanger any regular species in the environment.We only use E. coli and we will have disinfection after the experiment.

d. Risks to security through malicious misuse by individuals, groups, or countries?

No. We only have the directional optimization of promoters and use GFP to characterize them. GFP won't do any harm to the safety and health of the public and the environment.

5. If your project moved from a small- scale lab study to become widely used as a commercial/industrial product, what new risks might arise? (Consider the different categories of risks that are listed in parts a - d of the previous question.) Also, what risks might arise if the knowledge you generate or the met hods you develop became widely available? (Note: This is meant to be a somewhat open - ended discussion question.)

Using site-specific mutagenesis of genes might bring in safety problems, so strict treatment of waste is required in commercial production. Besides, the methods we use are widely used in the lab, and they won't cause any disadvantages if used properly.

6. Does your project include any design features to address safety risks? (For example: kill switches, auxotrophic chassis, etc.) Note that including such features is not mandatory to participate in iGEM, but many groups choose to include them.

No.

7. What safety training have you received (or plan to receive in the future)? Provide a brief description, and a link to your institution's safety training requirements, if available.

Yes,every member of our laboratory received biosafety training including standard laboratory operation and WHO Biosafety Manual training before the experiments. All members learnt about the "C3H3"which is well known in the college of chemistry and chemical engineering. http://210.34.15.138/rule/10384_2_c_18.pdf

8. Under what biosafety provisions will / do you work?

a. Please provide a link to your institution biosafety guidelines .

http://210.34.15.138/rule/10384_2_c_18.pdf

b. Does your institution have an Institutional Biosafety Committee, or an equivalent group? If yes, have you discussed your project with them? Describe any concerns they raised with your project, and any changes you made to your project plan based on their review.

No, we haven't discussed our project with an Institutional Biosafety Committee, but we discussed the safety problem with our instructors and confirmed that this project is safe enough if experimental rules are strictly observed.

c. Does your country have national biosafety regulations or guidelines? If so, please provide a link to these regulations or guidelines if possible.

http://english.biosafety.gov.cn/Center/200511/t20051101_13462.htm

d. According to the WHO Biosafety Manual, what is the BioSafety Level rating of your lab? (Check the summary table on page 3, and the fuller description that starts on page 9.) If your lab does not fit neatly into category 1, 2, 3, or 4, please describe its safety features [see 2013.igem.org/Safety for help].

Level 1.

e. What is the Risk Group of your chassis organism(s), as you stated in question 1? If it does not match the BSL rating of your laboratory, please explain what additional safety measures you are taking.

Risk group 1.

Faculty Advisor Name:

Fang Baishan

Faculty Advisor Signature:

iGEM Software Division Coding Practices Questionnaire

1. Are you using the iGEM Software repository at github.com/igemsof tware? If you have instead stored your code elsewhere, please explain where and why you have put it there. If your code is not in the iGEM repository, are you using any version control system such as Git, CVS, or SVN?

E' Note is a web software using SVN and Brick Worker is biobrick evaluation software which will use the iGEM Software repository at github.com/igemsoftware.

2.User Data

a. Does your software store any private data supplied by the user? (For example: the user's name and email address, passwords, DNA sequences, circuit designs, etc.) If yes, please describe what kind of data is stored. If no, skip the rest of this question and move on to question 3.

Yes, E' Note stores users' name, email address, passwords and experiment data that they submit. And Brick Worker doesn't store any private data.

b. What is the URL or IP address where the user's private data is stored? Where is the physical computer or hard drive that contains the user's private data?

E' Note's URL is http://sae.sina.com.cn/ that store the user's private data. It is the SinaAppEngine which is a Cloud platform made by sina corporation that contains the user's private data.

c. Please describe any encryption, password protection, etc. that you use to protect the user's data. (It is not mandatory to have such protections, but if you do, describe them.)

Because we rent the SinaAppEngine to make E' Note's application active, the user's private data is whole stored in it's Cloud storage which will be protected by a group of Safety professionals.

3. Does your software include any other security features? Please describe them here.

No, E' Note is in virtue of SinaAppEngine to make the most powerful protection and Brick Worker is to evaluate and analyze the biobrick sequence and dose not include any storage of the user's data.

4. Does your software let the user create a design by choosing parts/genes from a list/database, such as the Registry? If so, which lists/databases are included? Is there any restriction on which parts/ genes the user can choose?

Yes. For Brick Worker, in the primer design part, we allow the user to choose transcription factors and add transcription factor binding sites (TFBS) to the primer sequence, and the TFBS data is derived from RegulonDB.

5. Does your software allow users to write new data into any public lists or databases? If so, do you check the new data for errors before allowing it to be written?

No.

6. Does your software include any other features that encourage th e user to create safe designs? Please describe them here.

Yes. Our Brick Worker help user to locate the essential part of promoter and RBS so the user can design mutation in these sites to improve the quality of the biobricks and in the protein coding sequence optimization part our software automatically optimize the protein coding sequence to a higher expression level.

Lectures on Synthetic Biology

We collaborated with the Chemical Society of Fujian province to successfully hold a wide array of activities for a high school’s summer camp in our university. On July, 16th, 2013, lectures themed with synthetic biology and iGEM were made available to all the high school students in the summer camp. The number of high school students is more than three hundred.

The outline of this lectures included the basic concepts of synthetic biology, introduction of iGEM, its safety requirements and other experiment techniques. We tried our best to illustrate what is iGEM in great detail: from the very idea of synthetic biology to a potential and developing subject.

After the formal lectures, interaction part started in which the high school students could learn more biological knowledge with fun. Our team members interacted with the high school students actively: answering questions about synthetic biology, sharing experience of iGEM competition as well as further encouraging them to participate in iGEM.

In addition, we tried to emphasize the aspect of safety from two parts in our activities. One was what we would make. We made sure that the software or the bacteria which we used or created were harmless. The other was the safety of information. Our software which owned the security certificate would protect our users’ private information from violating./p>

During the lectures, we handed out questionnaires pertained to synthetic biology and iGEM to approximate 300 high school students. Contents of the questionnaires were mainly about the iGEM and the safety issues. The surveys indicated that about 82% high school students had a great interest in Synthetic Biology but few of them knows this international competition which urges us to do more to extend the influence and promote the development of iGEM in China. Notably, approximate 90% of the students were most concerned about safety issues. Hence, we believed that the first step to the popularization of iGEM among Chinese high schools was illustrating its safety to its potential participants.

这里缺两张图

Synthetic-Biology-Theme Campus Party

In order to propagate synthetic biology and iGEM, the Synthetic-Biology-Theme Campus Party was held in Guihua Building in our campus on July 17th 2013 from 2 pm to 5 pm oriented to the high school students in the summer camp.

Theme show of synthetic biology was the first section of the party. We introduced the basic conceptions of synthetic biology, its safety issues, as well as iGEM competition to our high school audience systematically. The attractive presentation won enthusiastic acclaim from audience as well as a bunch of feedbacks. In the same time, we emphasized the security of synthetic biology and our software again in this introduction. We all believed that the security policy was the cardinal and fundamental thing of iGEM.

The second section of our party was the game which included lantern riddles, finding differences in DNA, Fold-it, and Biological-Sha.

Guessing the lantern riddles was a traditional Chinese game. We handed out some synthetic biology riddles designed for biology education specifically. For example, one of riddles descripted the question as ‘the bottle which is full with alcohol, not used to light.’, and the answer corresponded to an alcohol lamp. Besides, some riddles were about the security facilities in labs. We prepared many gifts for students who got the correct answers and tried to recall their memory about that we introduce in the first section by this method.

Another game, Finding Differences in DNA, was a challenging game which required both perspicacity and memory. The object of this game was finding out all the tiny differences in a set of DNA pictures as soon as possible. Hard though it seemed, a whole bunch of high school students showed great interest in it. In the meanwhile, procedure of finding the differences helped them to familiarize with DNA sequences.

Fold-it was a computer game in which you can see the structure of a certain protein and fold it in order to make it achieve the most stable state. The score of this game was measured by the stability of the protein. (link: http://verycd.gdajie.com/topics/2817908/) We deem Fold-it a great approach to reverse the current trend that so many high school students were increasingly addicted to electronic games toward a better direction that games can also serve as a vehicle for imparting knowledge. Students could have fun while learning the determining factors of the stability of proteins.

The last but not least game was Synthetic-biology-sha, which was redesigned by us based on an extremely popular card game Sanguosha. The card in this game, for instance Bacterial Quorum Sensing card, was designed on the basis of theory of synthetic biology. While enjoying this card game, high school students actually learned some principles about synthetic biology. As well, some safety rules were introduced as long as playing the card games.

In the end, we took a photo of the autographs of the students. We will keep these busy but happy days on minds for our all lives. It will be a strong pushment for us to be better and do more effort in sharing advanced technology with young people and keeping everything safety and security!

Experience sharing

April 5th, 2013, we had the honor to welcome a former leader of iGEM team of Peking University, Haoqian Zhang to come to Xiamen University with the intention of deepening the communication between our two universities’ iGEM teams. During his visit, Zhang joined our two teams in the brainstorm and provided valuable comments on the team members’ ideas in terms of feasibility, safety, originality. Zhang also gave us a brief introduction about his own iGEM projects from which we benefited greatly.

“That which does not kill us makes us stronger.” Zhang said when he reminisced about the difficulties he confronted during conducting his iGEM project.

June 24th, 2013 witnessed another cheering gathering of communication and collaboration between Nanjing University’s iGEM team and us. After a short sightseeing tour around our unfailingly beautiful campus, we had a meeting during which the projects of both teams of Xiamen University, i.e., the cell oscillation circuit and the brick worker were introduced to Nanjing iGEMers. After that, an intense discussion was started on the feasibility and safety of these projects on which Nanjing iGEMers kindly offered their suggestions. The jubilant gathering ended with genuine blessings and encouragement for each other. Nanjing iGEMers, we hope to see you in the World Championship again!

Do you want to know more about our activities and iGEM? Come to Xiamen and have fun with XMU_Software iGEMers!

Wall painting of Synthetic Biology

One of the Xiamen University’s main tourist attractions, Furong Tunnel which attracted more than 1,000 tourist per day, was chosen as the place for wall painting of the slogan and symbol of our iGEM team. Epitomizing the core elements of iGEM software team -- software and synthetic biology, our Wall painting mainly represents a combination of biology and computer language. We believed that the safety needs a good cooperation between wet lab and dry lab. This Wall painting had attracted hundreds of passengers to take photos for it. Furthermore, some of them asked us for more information about iGEM when we were painting.

Our Human Practice activities turned out to be a brilliant and unquestionable success. It provided a bridge for communication among domestic iGEM teams, a platform for showcasing the definite charm of synthetic biology, a joyful gathering of all the former, present, and, of course, future iGEMers.