Selection and Validation of Reference Genes for RT-qPCR Analysis of Gene Expression in Nicotiana benthamiana upon Single Infections by 11 Positive-Sense Single-Stranded RNA Viruses from Four Genera

Differential Participation of Plant Ribosomal Proteins from the Small Ribosomal Subunit in Protein Translation under Stress

Upon exposure to biotic and abiotic stress, plants have developed strategies to adapt to the challenges imposed by these unfavorable conditions. The energetically demanding translation process is one of the main elements regulated to reduce energy consumption and to selectively synthesize proteins involved in the establishment of an adequate response. Emerging data have shown that ribosomes remodel to adapt to stresses. In Arabidopsis thaliana, ribosomes consist of approximately eighty-one distinct ribosomal proteins (RPs), each of which is encoded by two to seven genes. Recent research has revealed that a mutation in a given single RP in plants can not only affect the functions of the RP itself but can also influence the properties of the ribosome, which could bring about changes in the translation to varying degrees. However, a pending question is whether some RPs enable ribosomes to preferentially translate specific mRNAs. To reveal the role of ribosomal proteins from the small subunit (RPS) in a specific translation, we developed a novel approach to visualize the effect of RPS silencing on the translation of a reporter mRNA (GFP) combined to the 5'UTR of different housekeeping and defense genes. The silencing of genes encoding for NbRPSaA, NbRPS5A, and NbRPS24A in Nicotiana benthamiana decreased the translation of defense genes. The NbRACK1A-silenced plant showed compromised translations of specific antioxidant enzymes. However, the translations of all tested genes were affected in NbRPS27D-silenced plants. These findings suggest that some RPS may be potentially involved in the control of protein translation.

RefFinder: a web-based tool for comprehensively analyzing and identifying reference genes

Although many genes may serve as reference genes, they may cause different expression patterns by selecting different reference genes because no single gene is expressed consistently in all tested tissues of an organism under all environmental and developmental conditions. Thus, it is becoming increasingly important and necessary to identify suitable reference genes before performing gene expression analysis. Currently, there are several computational tools available for evaluating the stability of candidate reference genes. These tools are based on different statistical algorithms and may produce different rankings in stability within the same reference gene study. To date, the RefFinder is the only web-based tool available for comparing and evaluating housekeeping genes as candidates to be reference genes. In this tool, we integrated the four currently available computational programs (geNorm, NormFinder, BestKeeper, and the comparative ΔCt method) into a web-based tool for evaluating the stability and reliability of reference genes. According to the gene stability rankings derived from the four programs, we assigned an appropriate weight to each gene and calculated the geometric mean of weights for the final rankings. Aside from the overall ranking, a single program or combination of the four programs can be selected for evaluating the ranking of candidate reference genes. This tool has been widely used and validated by many research laboratories around the world. You may use this tool at http://www.heartcure.com.au/reffinder/  or  https://blooge.cn/RefFinder/ . You can also download this algorithm program from https://github.com/fulxie/RefFinder and setup on your own computer. RefFinder is developed by PHP. Users can deploy it to a Php-based server (Apache + PHP) and run it.