Molecular biology and coevolution

高效的生物合成在很大程度上取决于高效的RNA加工和翻译。我的研究方向是1)细菌中蛋白质编码基因与翻译机制的共同进化，2)真核生物中的内含子剪接。在细菌翻译过程中，1)mRNA上的sine - dalgarno （SD）序列和小亚单位rRNA （SSU）上的anti-SD （aSD）序列，2)意义密码子的使用和差异tRNA丰度，3)停止密码子的使用和释放因子（RF1和RF2）的差异丰度发生了协同进化。所有这些都涉及到一个基序信号及其解码器，即由aSD解码的SD，由tRNA解码的意义密码子，以及由释放因子解码的停止密码子。信号母题和它们的解码器之间的共同进化受到许多其他因素的干扰。SDs以及起始和终止密码子都可以嵌入到二级结构中，并且对各自的解码器不可见。选择的影响在高表达基因中比在低表达基因中更为明显。一个操纵子的第一个基因和后面的基因对SD/aSD配对的要求不同。终止密码子下游的不同核苷酸影响翻译终止效率。停止密码子可被trna误读，而感觉密码子可被释放因子误读。我们需要精确量化基序信号和解码器，以实现对它们之间关系的综合理解。我们利用RNA-Seq数据来表征3‘外核糖核酸酶持续降解产生的不同3’尾的mRNA、tRNA和SSU rRNA的丰度，并通过统计建模来量化它们之间的关系内含子剪接信号包括5‘和3’剪接位点和分支点位点，以及外显子和内含子剪接增强子。它们的信号强度也取决于二级结构、侧翼核苷酸和基因表达。许多酵母剪接体被无内含子mrna招募，因为这些mrna含有假剪接位点信号，尽管这些假信号在高度转录的基因中是被选中的。我们将1)利用位置权重矩阵和自组织图谱算法表征剪接信号强度；2)利用RNA-Seq数据测量剪接效率（SE），获得外显子-外显子连接（AEE）、外显子-内含子连接（AEI）和总mRNA （AT）的丰度，使SE = AEE/AT和AT = AEE + AEI; 3)建立剪接强度、二级结构、剪接增强子存在等因素对SE的影响模型。我们将首先将该方法应用于酵母（Saccharomyces cerevisiae），其中大多数含内含子的基因只有一个内含子，然后将该方法扩展到研究多细胞真核生物中含有多个内含子的基因。我们的研究不仅将提高翻译和剪接的知识，而且将有助于更好地设计工业上的生物合成。现有博士2人，硕士4人，本科生4人。

Efficient biosynthesis depends much on efficient RNA processing and translation. My research program focuses on 1) coevolution between protein-coding genes and translation machinery in bacteria, and 2) intron-splicing in eukaryotes. In bacterial translation, coevolution occurs between 1) Shine-Dalgarno (SD) sequences on mRNA and anti-SD (aSD) sequences on small subunit (SSU) rRNA, 2) sense codon usage and differential tRNA abundance, and 3) stop codon usage and differential abundance of release factors (RF1 and RF2). All these involve a motif signal and its decoders, i.e., SD decoded by aSD, sense codon by tRNA, and stop codon by release factors. Coevolution between the signal motifs and their decoders are confounded by many other factors. SDs, as well as start and stop codons, can all be embedded in a secondary structure and become invisible to their respective decoders. The effect of selection is more visible in highly expressed genes than in lowly expressed genes. Requirement of SD/aSD pairing differs between the first gene in an operon and the following genes. Different nucleotides downstream of stop codons affect translation terminate efficiency. Stop codon can be misread by tRNAs and sense codons misread by release factors. We need accurate quantification of motif signals and decoders to achieve an integrated understanding of their relationships. We have been using RNA-Seq data to characterize the abundance of mRNA, tRNA and SSU rRNA with different 3' tails generated by continuous degradation of 3' exoribonucleases, and statistical modeling to quantify their relationships Intron splicing signals consist of 5' and 3' splice sites and branchpoint sites, as well as exonic and intronic splice enhancers. Their signal strength also depends on secondary structure, flanking nucleotides, and gene expression. Many yeast spliceosomes are recruited by intronless mRNAs because these mRNAs harbor false splice site signals, although such false signals are selected against in highly transcribed genes. We will 1) characterize splicing signal strength by using position weight matrix and self-organizing map algorithms, 2) measure splicing efficiency (SE) by using RNA-Seq data to obtain abundance of exon-exon junctions (AEE), exon-intron junctions (AEI), and total mRNA (AT) so that SE = AEE/AT and AT = AEE + AEI, and 3) model how SE is affected by factors such as splicing strength, secondary structure, presence of splicing enhancers, etc. We will apply this method first to yeast (Saccharomyces cerevisiae) where most intron-containing genes have just one intron, and then extend the method to study genes with multiple introns in multicellular eukaryotes. Our research will not only advance knowledge of translation and splicing, but also lead to better design of biosynthesis in industry. Two PhD, 4 MSc and 4 undergrad student currently participate in the program.