The kinome of pineapple: catalog and insights into functions in crassulacean acid metabolism plants

Abstract

BackgroundCrassulacean acid metabolism (CAM) plants use water 20–80% more efficiently by shifting stomata opening and primary CO2 uptake and fixation to the nighttime. Protein kinases (PKs) play pivotal roles in this biological process. However, few PKs have been functionally analyzed precisely due to their abundance and potential functional redundancy (caused by numerous gene duplications).ResultsIn this study, we systematically identified a total of 758 predicted PK genes in the genome of a CAM plant, pineapple (Ananas comosus). The pineapple kinome was classified into 20 groups and 116 families based on the kinase domain sequences. The RLK was the largest group, containing 480 members, and over half of them were predicted to locate at the plasma membrane. Both segmental and tandem duplications make important contributions to the expansion of pineapple kinome based on the synteny analysis. Ka/Ks ratios showed all of the duplication events were under purifying selection. The global expression analysis revealed that pineapple PKs exhibit different tissue-specific and diurnal expression patterns. Forty PK genes in a cluster performed higher expression levels in green leaf tip than in white leaf base, and fourteen of them had strong differential expression patterns between the photosynthetic green leaf tip and the non-photosynthetic white leaf base tissues.ConclusionsOur findings provide insights into the evolution and biological function of pineapple PKs and a foundation for further functional analysis of PKs in CAM plants. The gene duplication, expression, and coexpression analysis helped us to rapidly identify the key candidates in pineapple kinome, which may play roles in the carbon fixation process in pineapple and help engineering CAM pathway into C3 crops for improved drought tolerance.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1389-z) contains supplementary material, which is available to authorized users.

The wild strawberry kinome: identification, classification and transcript profiling of protein kinases during development and in response to gray mold infection

“…Over 600 RLK genes are found in Arabidopsis, making up > 2% of its genome, and almost 61% of the Arabidopsis kinome [26]. The proportion of RLKs is also over 50% of the kinome in other species including pineapple (63.3%), soybean (67.4%), and grapevine (74.6%) [3,27,28]. In this study, a total of 639 RLK genes were identified, accounting for about 67% of the woodland strawberry kinome, which is consistent with the species mentioned above.…”

“…Segmental duplication events were the main cause for the expansion of the soybean kinome [3]. Segmental, tandem, or whole-genome duplication events have been key in the expansion of the gene families in both the grapevine and pineapple kinomes, especially in the RLK group [27,28].…”

“…To report the predicted functions of woodland strawberry PK protein translations, the gene ontology (GO) annotations for strawberry PKs were downloaded from the Gene Ontology Consortium (http://www.geneontology.org/) [27].…”

The sugarcane and sorghum kinomes: insights into evolutionary expansion and diversification

“…Because RLCK family members do not contain extracellular and transmembrane domains (Gao and Xue, 2012;Zulawski et al, 2014), these proteins are generally involved in more specific processes (Jurca et al, 2008). In addition to disease resistance, RLCK proteins have been shown to be related to plant growth, immune responses (Yan et al, 2018;Zhu et al, 2018a), and vegetative development (Jurca et al, 2008;Gao and Xue, 2012). Together with RLCK family members, DLSV family members were found to be differentially expressed in soybean tissues in stress experiments (Liu et al, 2015).…”

Model approaches to advance crassulacean acid metabolism system integration

“…Nevertheless, one must be aware that there are multiple levels of control. Genes that have not adopted a CAM‐specific diel expression pattern can have a crucial role in CAM function if the protein activities are modified at other levels of regulatory processes, including but not limited to post‐translational modifications (Yang et al , ; Zhu et al , ).…”