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Background  Trichomes and phenylpropanoid-derived phenolics are structural and chemical protection against many adverse conditions. Their production is regulated by a network that includes a TTG1/bHLH/MYB tri-protein complex in Arabidopsis.  CSN5a , encoding COP9 signalosome subunit 5a, has also been implicated in trichome and anthocyanin production; however, the regulatory roles of CSN5a in the processes through interaction with the tri-protein complex has yet to be investigated.    Results  In this study, a new  csn5a  mutant,  sk372 , was recovered based on its altered morphological and chemical phenotypes compared to wild-type control. Mutant characterization was conducted with an emphasis on trichome and phenylpropanoid production and possible involvement of the tri-protein complex using metabolite and gene transcription profiling and scanning electron microscopy. Seed metabolite analysis revealed that defective CSN5a led to an enhanced production of many compounds in addition to anthocyanin, most notably phenylpropanoids and carotenoids as well as a glycoside of zeatin. Consistent changes in carotenoids and anthocyanin were also found in the  sk372  leaves. In addition, 370 genes were differentially expressed in 10-day old seedlings of  sk372  compared to its wild type control. Real-time transcript quantitative analysis showed that in  sk372 ,  GL2  and tri-protein complex gene  TT2  was significantly suppressed ( p  < 0.05) while complex genes  EGL3  and  GL3  slightly decreased ( p  > 0.05). Complex genes  MYB75, GL1  and flavonoid biosynthetic genes TT3 and TT18 in  sk372  were all significantly enhanced. Overexpression of  GL3  driven by cauliflower mosaic virus 35S promotor increased the number of single pointed trichomes only, no other phenotypic recovery in  sk372 .    Conclusions  Our results indicated clearly that COP9 signalosome subunit CSN5a affects trichome production and the metabolism of a wide range of phenylpropanoid and carotenoid compounds. Enhanced anthocyanin accumulation and reduced trichome production were related to the enhanced  MYB75  and suppressed  GL2  and some other differentially expressed genes associated with the TTG1/bHLH/MYB complexes.    Electronic supplementary material  The online version of this article (10.1186/s12870-018-1347-9) contains supplementary material, which is available to authorized users.

bmc plant biology

COP9 signalosome subunit 5A affects phenylpropanoid metabolism, trichome formation and transcription of key genes of a regulatory tri-protein complex in Arabidopsis