Opposing roles of RUBCN isoforms in autophagy and memory B cell generation

RUBCN (also known as Rubicon) was originally identified as a negative regulator of autophagy, a process by which cells degrade and recycle damaged components or organelles and that requires the activity of the class III PI3K VPS34 and the mTORC1 protein complex. Here, we characterized the role of a shorter isoform, RUBCN¹⁰⁰, as an autophagy-promoting factor in B cells. RUBCN¹⁰⁰ was translated from alternative translation initiation sites and lacked the RUN domain of the longer, previously characterized RUBCN¹³⁰ isoform. Specific deficiency of RUBCN¹³⁰ in B cells enhanced autophagy, which promoted memory B cell generation. In contrast to RUBCN¹³⁰, which is localized in late endosomes and lysosomes and suppresses the enzymatic activity of VPS34, an effect thought to mediated by its RUN domain, RUBCN¹⁰⁰ was preferentially located in early endosomes and enhanced VPS34 activity, presumably because of the absence of the RUN domain. Furthermore, RUBCN¹⁰⁰, but not RUBCN¹³⁰, enhanced autophagy and suppressed mTORC1 activation. Our findings reveal that the opposing roles of two RUBCN isoforms are critical for autophagy regulation and memory B cell differentiation.