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A Computer-aided Temperature-response Regulatory RNA Design

CHEN Huaiqing1, CHEN Zheqin2, FAN Xiao2, LI Renkuan2, LI Tianyi1, LI Zhangqinang1, PENG Liying2, SUN Xiaochen2, WANG Xuan2, WANG Zhipeng2, XIE Hengyi1, YANG Tianfang2, SHI Binbin2,※ and DING Hongxu2,※

 

1. School of Life Science, Tsinghua University
2. iGEM Tsinghua-D team, Tsinghua University

    ※. To whom correspondence should be addressed, SHI Binbin, ltbyshi@gmail.com; DING Hongxu, poulainding@163.com. 

   This article can be downloaded at HERE (PDF).

   Supporting online materials can be downloaded at HERE (PDF).

   A demo for RNAThermo can be found at HERE.

   RNAThermo can be downloaded at HERE.

Abstract  The first software that designs temperature-sensing regulatory RNA – RNAThermo is presented in this article.  Parameters were set and several temperature-sensing regulatory RNA sequences were given by the RNAThermo.  The designed RNAs have been verified both as to on the structural and functional aspects.  RNAThermo’s potential application in the fermentation industry is discussed.

Keywords: RNA Thermometer, Computer, Design

Introduction

In addition to exploration, explanation and prediction, the ultimate goal of science is creation.  In the field of life science, enthusiasm towards creation originates the synthetic biology.  During the last decade, numerous artificial biological networks had been made by rearranging the exited biological macromolecules.  Recently, creation of the macromolecules inside biological networks emerges as a hotspot.  Because of structural simplicity and manipulation convenience, RNA becomes an ideal model for conducting such researches.  In this article, the first software that designs temperature-sensing regulatory RNA - RNAThermo is reported.  Structural and functional verifications of the designed RNATs were made.  RNAThermo’s potential application in the fermentation industry is discussed:  the software provides a new method for achieving controlled expression of products in the fermentation industry.

RNA Thermometer (RNAT)

Residing in the 5’ untranslated region (5’UTR) of the entire mRNA, the RNA thermometer (RNAT) is a kind of temperature-sensing sequence.  As the environmental temperature changes, the RNAT folds into a series of different secondary structures.  Several of the structures block ribosomes’ access to the mRNA thus hinder translation (referred to as unmelted structure).  Other structures cause ribosomes’ binding to the mRNA and the initiation of translation (referred to as melted structure).  By shifting from the two kinds of structures, the RNAT regulates gene expression in the level of translation (1). 

The software RNAThermo designs RNATs that meet the given parameters

Based on biological and physical principles, adapting computer algorithms, TNAThermo designs RNATs that meet the given parameters.  What the user tells the software are the regulation temperature, the structure (both unmelted structure and melted structure) of the RNAT and the SD sequence position of the RNAT.  RNAThermo gives the sequences of RNATs that fulfill these requirements. 

The design of RNATs based on biological principles

The principle behind the RNATs’ response to temperature is fundamental: At low temperatures, the sequence that binds to ribosomes will be trapped in a hairpin structure.  Increasing temperature destabilizes the structure such that the trapped sequence becomes accessible, allowing translation to be initiated.  The following (Figure 1) is the schematic diagram (2):

 

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  Figure 1.  Structural change of RNAT’s according to the environmental temperature.  The SD stands for Shine-Dalgarno sequence, which is recognized and bind by ribosome to initiate translation.  The AUG stands for start codon, from where the translation begins.

  One example for this mechanism is the regulation of E.Coli’s rpoH gene (Figure 2).  Responding to environmental temperature change, rpoH gene regulates the expression of the heat shock protein.  Low temperature (30℃) induces a bend in the ribosome-binding site (RBS)-associated downstream box (DB) region, thereby interfering with ribosome binding.  High temperature (42℃) disrupts the bend and initiates the process of translation (3).

  

  Figure 2.  a. Formation of stem III in the rpoH transcript at low temperatures (30 °C) induces a bend in the ribosome-binding site (RBS)-associated downstream box (DB) region, thereby interfering with ribosome binding.  b. A rise in temperature to 42 °C opens stem III and stem I of the rpoH mRNA, liberates the AUG start codon and DB region, facilitates ribosome binding.

  Inspired by such a mechanism, our group designed a series of RNATs whose SD sequence will have trap-release structural change according to the environmental temperature.  The following is the schematic diagram of the RNATs we designed (Figure 3):

  

  Figure 3.  Schematic diagram of the RNATs we designed.  The red box indicates the SD sequence.

   

  The design of RNATs based on physical principles

  To give RNAT sequences that meet the given parameters, the central problem is to predict RNATs’ secondary structure at a given temperature.  Two methods are adapted according to the computer algorithm’s requirement. 

  One principle adapted in predicting RNA secondary structure is free energy minimization (4).  A secondary structure with the least free energy is regarded to be the optimal solution (5).

  Another principle adapted here is the partition function method (6).  Rather than give one definite structure as the free energy minimization method, the partition function gives the probability of each secondary structure’s appearance.  In the following equation, Q stands for the partition function and P (structure) stands for the probability of one specific structure’s appearance.

  

  The design of RNATs adapting computer algorithms

  The software RNAThermo for designing an RNA thermometer is presented.  RNAThermo is based on the Vienna RNA Package, which is a program for RNA Secondary Structure Prediction and Comparison (7).

  Before introducing RNAThermo, this is the basic RNAT design problem: given regulation temperature, the structure of the RNAT (both unmelted structure S1 and melted structure S2) and the SD sequence position of the RNAT, find an RNAT whose SD sequence will be released from the hairpin structure above the desired temperature.

  A three-stage algorithm is designed to solve the problem (workflow is present in Figure 4):  A set of sequences that fold into the S1 structure at low temperature is found.  Sequences that cannot fold into the S2 structure at the high temperature are screened out.  After these two stages, sequences meet the structural requirement are obtained.  However, regulation temperatures of the obtained sequences remain unmeasured.  The third stage is designed to screen RNATs to meet the temperature requirement.

  

  Figure 4.  Workflow of designing an RNA thermometer

  Verification of the designed RNATs’ secondary structure

  The first step in verification the in silico design is testing the designed structure in vitro.  In-line probing method is adapted to measure the RNATs’ structure (10).  The results are as shown in Figure 5.

   

  

  Figure 5  Result of the in-line probing. The sequence of the RNAT is 5’-GAAUACAUGUUAAUUAUGCCAUCCAGGCAUACAGAAGAAGUUAAU-3’ and the regulation temperature of the RNAT is 39.5℃. RNAT loaded in lane 1, 2, 3 was incubated at 46℃ for 20h, 26h and 32h. RNAT loaded in lane 4, 5, 6 was incubated at 42℃ for 20h, 26h and 32h. RNAT loaded in lane 7, 8, 9 was incubated at 37℃ for 20h, 26h and 32h. The red boxes mark sections that melt when temperature rises.

  When temperature rises, sections marked by the red boxes melt thus bands appear. The results show strong evidence that the designed RNATs can fold into desired secondary structure.

   

  Verification of the designed RNATs’ temperature-sensing regulatory function

  Then, rectification of the temperature-response regulatory function in vivo should be taken in verification of the in silico design.  GFP is adapted as reporter gene in measuring the RNATs’ temperature-response regulatory function.  The results are shown in Figure 6.

  

  Figure 6  Schematic diagram of ‘RNAT + GFP’ gene.

  E.Coli were cultured in 30℃ until they reached stationary phrase. Then the E.Coli were divided into two flasks. For the experimental group, a 45℃ heat shock was exerted to the E.Coli. For the control group, the temperature remained 30℃. Photos were taken after a two-hour adjustment. Two RNAT sequences were tested and the results are shown in Figure 8 and Figure 9.

   

  Potential Application in Fermentation Industry

  Computer aided RNAT design provides a new method for achieving controlled expression of products in fermentation industry.  Engineered microorganisms sense a temperature signal and initiate the regulation.  The results are shown in Figure 7.

  
  Figure 7

   

  Reference
  (1). Jens Kortmann and Franz Narberhaus.  Bacterial RNA thermometers: molecular zippers and switches.  NATURE REVIEWS MICROBIOLOGY, VOLUME 10, 265, APRIL 2012
  (2). Birgit Klinkert and Franz Narberhaus.  Microbial thermosensors.  Cell. Mol. Life Sci.  (2009) 66:2661–2676
  (3). Miyo Terao Morita, Yoshiyuki Tanaka, Takashi S. Kodama, Yoshimasa Kyogoku,
  Hideki Yanagi and Takashi Yura.  Translational induction of heat shock transcription factor sigma32: evidence for a built-in RNA thermosensor..  Genes Dev. 1999 13: 655-665
  (4). David H. Mathews.  Revolutions in RNA Secondary Structure Prediction.  J. Mol. Biol. (2006) 359, 526–532
  (5). David H Mathews and Douglas H Turner.  Prediction of RNA secondary structure by free energy minimization.  Current Opinion in Structural Biology 2006, 16:270–278
  (6). J. S. McCASKlLL.  The Equilibrium Partition Function and Base Pair Binding Probabilities for RNA Secondary Structure.  Biopolymers, Vol. 29,1105-1119 (1990)
  (7). http://www.tbi.univie.ac.at/~ivo/RNA/
  (8). http://www.tbi.univie.ac.at/~ivo/RNA/man/RNAfold.html
  (9). L. Hofacker, W. Fontan.  Fast folding and comparison of RNA secondary structures. Monatshefte fur Chemie , 125, 167-188.
  (10). In-Line Probing Analysis of Riboswitches.Elizabeth E.  Regulski and Ronald R. Breaker.  NATURE PROTOCOL EXCHANGE http://www.nature.com/protocolexchange/protocols/1889

   

  Acknowledgement

  Thank Prof. CHEN Guoqiang, Prof. SUN Zhirong and Prof. DAI Junbiao for their guidance in the project.  Thank Prof. Tom Kellie for his revision of the PPT and the report.  Thanks Dr. YIN Ping and Dr. QU Peng for their help in the RNA experiments.  Thanks FU Xiaozhi and LI Teng for their help in the molecular biology experiments.