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Background  The  Arabidopsis microRNA156  ( miR156 ) regulates 11 members of the  SQUAMOSA PROMOTER BINDING PROTEIN LIKE  ( SPL ) family by base pairing to complementary target mRNAs. Each  SPL  gene further regulates a set of other genes; thus, miR156 controls numerous genes through a complex gene regulation network. Increased axillary branching occurs in transgenic  Arabidopsis  overexpressing  miR156b , similar to that observed in loss-of-function  max3  and  max4  mutants with lesions in carotenoid cleavage dioxygenases.  Arabidopsis miR156b  was found to enhance carotenoid levels and reproductive shoot branching when expressed in  Brassica napus,  suggesting a link between  miR156b  expression and carotenoid metabolism. However, details of the miR156 regulatory network of  SPL  genes related to carotenoid metabolism are not known.    Results  In this study, an  Arabidopsis  T-DNA enhancer mutant,  sk156 , was identified due to its altered branching and trichome morphology and increased seed carotenoid levels compared to wild type (WT) ecovar Columbia. Enhanced  miR156b  expression due to the 35S enhancers present on the T-DNA insert was responsible for these phenotypes. Constitutive and leaf primodium-specific expression of a miR156-insensitive (mutated)  SPL15  ( SPL15m ) largely restored WT seed carotenoid levels and plant morphology when expressed in  sk156 . The  Arabidopsis  native miR156-sensitive  SPL15  ( SPL15n ) and  SPL15m  driven by a native  SPL15  promoter did not restore the WT phenotype in  sk156 . Our findings suggest that  SPL15  function is somewhat redundant with other SPL family members, which collectively affect plant phenotypes. Moreover, substantially decreased  miR156b  transcript levels in  sk156  expressing  SPL15m,  together with the presence of multiple repeats of SPL-binding GTAC core sequence close to the  miR156b  transcription start site, suggested feedback regulation of  miR156b  expression by SPL15. This was supported by the demonstration of specific  in vitro  interaction between DNA-binding SBP domain of SPL15 and the proximal promoter sequence of  miR156b.Conclusions  Enhanced  miR156b  expression in  sk156  leads to the mutant phenotype including carotenoid levels in the seed through suppression of  SPL15  and other SPL target genes. Moreover, SPL15 has a regulatory role not only for downstream components, but also for its own upstream regulator  miR156b .

Arabidopsis mutant sk156 reveals complex regulation of SPL15 in a miR156-controlled gene network