Transcriptome-wide identification and characterization of the Rab GTPase family in mango

Abstract

The Rab GTPase family plays a vital role in several plant physiological processes including fruit ripening. Fruit softening during ripening involves trafficking of cell wall polymers and enzymes between cellular compartments.Mango, an economically important fruit crop, is known for its delicious taste, exotic flavour and nutritional value.So far, there is a paucity of information on the mango Rab GTPase family. In this study, 23 genes encoding Rab proteins were identified in mango by a comprehensive in silico approach. Sequence alignment and similarity tree analysis with the model plant Arabidopsis as a reference enabled the bona fide assignment of the deduced mango proteins to classify into eight subfamilies. Expression analysis by RNA-Sequencing (RNA-Seq) showed that the Rab genes were differentially expressed in ripe and unripe mangoes suggesting the involvement of vesicle trafficking during ripening. Interaction analysis showed that the proteins involved in vesicle trafficking and cell wall softening were interconnected providing further evidence of the involvement of the Rab GTPases in fruit softening.Correlation analyses showed a significant relationship between the expression level of the RabA3 and RabA4 genes and fruit firmness at the unripe stage of the mango varieties suggesting that the differences in gene expression level might be associated with the contrasting firmness of these varieties. This study will not only provide new insights into the complexity of the ripening-regulated molecular mechanism but also facilitate the identification of potential Rab GTPases to address excessive fruit softening. Keywords Fruit ripening, Gene expression, Mango, Rab GTPase, Vesicle trafficking isoelectric point (pI) of the Rabs were predicted by EMBOSS Pepstats (https://www.ebi.ac.uk/Tools/seqstats/emboss_pepstats/). The predicted mango Rab proteins were assigned to subfamilies on the basis of their similarity to the sequences of Arabidopsis [11] and were named according to their closest similarity to Arabidopsis proteins. Where more than one mango Rab GTPase was present in the same subclade, a nomenclature based on numbers was adopted [9]. Sequence and Similarity Tree AnalysisModel plants Arabidopsis thaliana and tomato (Solanum lycopersicum) were used for comparative analysis.Arabidopsis thaliana Rab protein sequences were obtained from the Arabidopsis information resource (TAIR; https://www.arabidopsis.org). Members of the Rab GTPase family in tomato were identified from the Sol Genomics Network Browser (http://solgenomics.net) through BLASTP searches. Protein sequences were used for sequence and similarity analysis facilitating their classification in different families and subfamilies. The multiple sequence alignment was conducted using the software MultAlin (http://multalin.toulouse.inra.fr/multalin) [22]. A similarity tree was produced by the neighbour-joining (NJ) method [23] using the MEGA software (version 6.0) [24]. The reliability of the trees was examined using 1000 bootstrap replicates. Percentage con...

Transcriptome Analysis Reveals Potential Mechanism in Storage Protein Trafficking within Developing Grains of Common Wheat

“…This suggested intracellular protein quality control within the ER. GTPase activity has been approved as an important regulator in gluten quality characteristics, through controlling ER-to-Golgi vesicle trafficking [ 59 , 60 , 61 , 62 , 63 ]. TraesCS1A02G137213 linked with GO: 0043547 (positive regulation of GTPase activity) showed a higher expression at 10 DPA (cell division phase), which decreased at 30 DPA.…”

“…This suggested the role of storage protein activator SPA, in the key functional mechanism to maintain a homeostasis supply of nutrients between the maternal cells and the starchy endosperm, and linked with the serine-to-cysteine biosynthesis process. Rab GTPase has been approved in different quality characteristics of mango, and others [ 63 , 87 ]. Therefore, further investigation is needed to improve our knowledge.…”

“…The accumulation of protein bodies is taken either directly within the lumen of the ER or through the Golgi apparatus into the vacuole [ 27 , 28 , 29 , 30 , 31 , 59 , 60 , 61 , 62 , 63 , 70 , 98 ]. Here, we proposed a model through combining our results and previous successful works, which could be used to test how trafficking of GSP within the developing grain improves the wheat grain end-product quality ( Figure 13 ).…”

Transcriptome profiling of abiotic responses to cold and drought stress of Cinnamomum kanehirae

“…High-throughput sequencing is an important technique for studying plant molecules, since it enables the identification and characterization of new large-scale transcriptional data (Martin and Wang 2011;Lawson et al 2020). In recent years, increasing numbers of researchers have used transcriptome sequencing to study changes in the levels of expression of drought-tolerant and cold-tolerant genes in plants (Dong et al 2014;Yang et al 2015).…”

Identification of Rab family genes and functional analyses of LmRab5 and LmRab11A in the development and RNA interference of Locusta migratoria

“…So far, 11 different Rab genes in Saccharomyces cerevisiae (Lazar et al ., 1997), 29 in Caenorhabditis elegans (Bock et al ., 2001), 70 in Homo sapiens (Zerial & McBride, 2001), 57 in Arabidopsis thaliana (Vernoud et al ., 2003), 90 in Entamoeba histolytica (Nakano et al ., 2005), 33 in Drosophila melanogaster (Zhang et al ., 2007), 67 in Populus trichocarpa (Zhang et al ., 2018a), and 23 in Mangifera sp. (Lawson et al ., 2020) have been characterized. However, to date investigation of Rab family genes has not been reported for nonmodel insect species and our knowledge on functional roles of various Rab family genes is still very limited.…”