Nubbin isoform antagonism governs Drosophila intestinal immune homeostasis

Abstract

Gut immunity is regulated by intricate and dynamic mechanisms to ensure homeostasis despite a constantly changing microbial environment. Several regulatory factors have been described to participate in feedback responses to prevent aberrant immune activity. Little is, however, known about how transcriptional programs are directly tuned to efficiently adapt host gut tissues to the current microbiome. Here we show that the POU/Oct gene nubbin (nub) encodes two transcription factor isoforms, Nub-PB and Nub-PD, which antagonistically regulate immune gene expression in Drosophila. Global transcriptional profiling of adult flies overexpressing Nub-PB in immunocompetent tissues revealed that this form is a strong transcriptional activator of a large set of immune genes. Further genetic analyses showed that Nub-PB is sufficient to drive expression both independently and in conjunction with nuclear factor kappa B (NF-κB), JNK and JAK/STAT pathways. Similar overexpression of Nub-PD did, conversely, repress expression of the same targets. Strikingly, isoform co-overexpression normalized immune gene transcription, suggesting antagonistic activities. RNAi-mediated knockdown of individual nub transcripts in enterocytes confirmed antagonistic regulation by the two isoforms and that both are necessary for normal immune gene transcription in the midgut. Furthermore, enterocyte-specific Nub-PB expression levels had a strong impact on gut bacterial load as well as host lifespan. Overexpression of Nub-PB enhanced bacterial clearance of ingested Erwinia carotovora carotovora 15. Nevertheless, flies quickly succumbed to the infection, suggesting a deleterious immune response. In line with this, prolonged overexpression promoted a proinflammatory signature in the gut with induction of JNK and JAK/STAT pathways, increased apoptosis and stem cell proliferation. These findings highlight a novel regulatory mechanism of host-microbe interactions mediated by antagonistic transcription factor isoforms.

JNK-dependent intestinal barrier failure disrupts host–microbe homeostasis during tumorigenesis

“…Our data also demonstrate that microbial clearance reduces proliferative and inflammatory signals in tumor intestine with a decreased stem cell activity, indicating the dysbiotic microbiome create a proinflammatory environment that promotes tumor growth. Consistent with this, studies in insect models suggested that microbial dysbiosis by dysregulating the immune regulator Nub-PB, or oral infection with commensals promotes proinflammatory signatures and the activation of JAK/STAT and JNK signaling in the intestine (52,53). It has also been shown that aging-related intestinal dysbiosis occurs before intestinal barrier dysfunction (36,37).…”

The POU/Oct Transcription Factor Nubbin Controls the Balance of Intestinal Stem Cell Maintenance and Differentiation by Isoform-Specific Regulation

“…Thus, well-tuned expression of the two Nub protein isoforms is necessary for normal ISC proliferation and differentiation. Moreover, it was recently reported that Nub-PB and Nub-PD regulate the expression of immune genes in gut ECs in an antagonistic manner ( Lindberg et al., 2018 ), pointing to the possibility that Nub-PB and Nub-PD play important roles in controlling epithelial renewal in the gut upon infection. This is supported by the fact that in nub 1 mutants, ISC proliferation was considerably reduced ( Figures 6 A–6H), suggesting that Nub-PD is also required for infection-induced stem cell division.…”

“…Alternative transcripts have earlier been reported to be expressed from the nub gene ( Ng et al., 1995 ), and annotation of the Drosophila genome suggested at least two independent transcripts termed nub-RB and nub-RD (FlyBase: FBgn0085424 ). Recent experimental evidence has revealed that two protein isoforms, Nub-PB and Nub-PD, are expressed in Drosophila ( Dantoft et al., 2013 , Lindberg et al., 2018 ). Transcription of the nub gene initiates at two major promoters that are separated by more than 30 kB.…”

Anatomy and Physiology of the Digestive Tract of Drosophila melanogaster

“…The Toll pathway contributes to resistance to oral infection by Drosophila C virus, but the protection mechanism, whether physiological or immune, is not yet known ( Ferreira et al 2014 ). Transcriptionally, transcription factors such as Nub coordinate the response to bacterial infection ( Lindberg et al 2018 ). The second inducible host defense mechanism is the production of ROS by Duox or the NADPH oxidase Nox ( Ha et al 2005 ; Jones et al 2013 ).…”