MINI-REVIEW Small RNA regulators in bacteria: powerful tools for metabolic engineering and synthetic biology Zhen Kang & Chuanzhi Zhang & Junli Zhang & Peng Jin & Juan Zhang & Guocheng Du & Jian Chen Received: 8 December 2013 /Revised: 22 January 2014 /Accepted: 23 January 2014 # Springer-Verlag Berlin Heidelberg 2014 Abstract Small RNAs, a large class of ancient posttranscrip- tional regulators, have recently attracted considerable atten- tion. A plethora of small RNAs has been identified and characterized, many of which belong to the major small non- coding RNA (sRNA) or riboswitch families. It has become increasingly clear that most small RNAs play critical regula- tory roles in many processes and are, therefore, considered to be powerful tools for metabolic engineering and synthetic biology. In this review, we describe recent achievements in the identification, characterization, and application of small RNAs. We give particular attention to advances in the design and synthesis of novel sRNAs and riboswitches for metabolic engineering. In addition, a novel strategy for hierarchical control of global metabolic pathways is proposed. Keywords Small RNA . Riboswitch . Gene expression . Posttranscriptional regulation . Metabolic engineering . Synthetic biology Introduction In recent years, it has become evident that posttranscriptional regulation mediated by RNA regulators is critical to many cellular processes in both prokaryotic and eukaryotic king- doms (Grosshans and Filipowicz 2008). Hundreds of candi- date regulatory RNA genes in many bacteria have been pre- dicted and characterized using a variety of experimental tools, such as direct labeling and RNA sequencing, Rnomics (shot- gun cloning), DNA microarray, and Genomic SELEX tech- nologies and bioinformatic approaches (Gottesman 2005; Li et al. 2013b; Livny and Waldor 2007; Pichon and Felden 2008). RNA regulators have been exploited for use in molec- ular engineering and compared with other regulatory systems; posttranscriptional regulation using small RNAs is cost- effective (Altuvia and Wagner 2000). Furthermore, cells are able to use these small molecules to rapidly respond to various environmental signals and stresses. According to their mech- anisms of action, these RNA regulators can be divided into two main classes: small noncoding RNAs (sRNAs) and riboswitches. In this review, we summarize recent advances in the discovery, design, synthesis, and application of sRNAs and riboswitches. We also predict future directions for the application of small RNA regulators in metabolic engineering and synthetic biology. sRNAs in bacteria and their mechanisms of action Over the past decades, sRNAs in bacteria (especially in Escherichia coli) have been predicted and experimentally Z. Kang : J. Zhang : G. Du : J. Chen Synergetic Innovation Center of Food Safety and Nutrition, Wuxi 214122, China Z. Kang : C. Zhang : J. Zhang : P. Jin : J. Zhang : G. Du : J. Chen The Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China G. Du The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China Z. Kang : J. Zhang : G. Du : J. Chen Synergy Innovation Center of Modern Industrial Fermentation, Wuxi 214122, China J. Chen (*) National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China e-mail: jchen@jiangnan.edu.cn Z. Kang (*) Yixing Union Biochemical Co., Ltd., Wuxi 214203, China e-mail: zkang@jiangnan.edu.cn Appl Microbiol Biotechnol DOI 10.1007/s00253-014-5569-y