title: Number variation of high stability regions is correlated with gene functions.
abstract: Various regulatory elements in messenger RNAs (mRNAs) carrying the secondary structure play important roles in a wide range of expression processes. Numerous recent works have focused on the discovery of these functional elements that contain the conserved mRNA structures. However, to date, regions with high structural stability have been largely overlooked. In this study, we defined high stability regions (HSRs) in the coding sequences (CDSs) in bacteria based on the normalized folding free energy. We found that CDSs had high number of HSRs, and these HSRs showed high structural context robustness compared with random sequences, indicating a direct selective constraint imposed on HSRs. A reduced ribosome speed was detected near the start position of HSR, implying a possibility that HSR acted as obstacle to drive translational pausing that coordinated protein synthesis. Interestingly, we found that genes with high HSR density were enriched in the processes of translation, protein folding, and cell division. In addition, essential genes exhibited higher HSR density than nonessential genes. Overall, our study presented the previously unappreciated correlation between the number variation of HSRs and cellular processes.
authors: College of life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi, China.
authors: Yuanhui
authors: Y
authors: Mao
authors: Qian
authors: Q
authors: Li
authors: Wangtian
authors: W
authors: Wang
authors: Peiquan
authors: P
authors: Liang
authors: Shiheng
authors: S
authors: Tao
mesh_terms: D056915:DNA Copy Number Variations; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D004755:Enterobacteriaceae / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D009690:Nucleic Acid Conformation; D016366:Open Reading Frames; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism
chemical_list: D004269:DNA, Bacterial; D012333:RNA, Messenger