Cellular and molecular organization of the Drosophila foregut.

The animal foregut is the first tissue to encounter ingested food, bacteria, and viruses. We characterized the adult Drosophila foregut using transcriptomics to better understand how it triages consumed items for digestion or immune response and manages resources. Cell types were assigned and validated using GFP-tagged and Gal4 reporter lines. Foregut-associated neuroendocrine cells play a major integrative role by coordinating gut activity with nutrition, the microbiome, and circadian cycles; some express clock genes. Multiple epithelial cell types comprise the proventriculus, the central foregut organ that secretes the peritrophic matrix (PM) lining the gut. Analyzing cell types synthesizing individual PM layers revealed abundant mucin production close to enterocytes, similar to the mammalian intestinal mucosa. The esophagus and salivary gland express secreted proteins likely to line the esophageal surface, some of which may generate a foregut commensal niche housing specific gut microbiome species. Overall, our results imply that the foregut coordinates dietary sensing, hormonal regulation, and immunity in a manner that has been conserved during animal evolution.

Chromatin and gene expression changes during female Drosophila germline stem cell development illuminate the biology of highly potent stem cells.

Highly potent animal stem cells either self renew or launch complex differentiation programs, using mechanisms that are only partly understood. Drosophila female germline stem cells (GSCs) perpetuate without change over evolutionary time and generate cystoblast daughters that develop into nurse cells and oocytes. Cystoblasts initiate differentiation by generating a transient syncytial state, the germline cyst, and by increasing pericentromeric H3K9me3 modification, actions likely to suppress transposable element activity. Relatively open GSC chromatin is further restricted by Polycomb repression of testis or somatic cell-expressed genes briefly active in early female germ cells. Subsequently, Neijre/CBP and Myc help upregulate growth and reprogram GSC metabolism by altering mitochondrial transmembrane transport, gluconeogenesis, and other processes. In all these respects GSC differentiation resembles development of the totipotent zygote. We propose that the totipotent stem cell state was shaped by the need to resist transposon activity over evolutionary timescales.

Most animals are made up of two cell types: germline stem cells, which give rise to reproductive cells (egg and sperm) and pass their DNA to the next generation, and somatic cells, which make up the rest of the body. Transposable elements ­ fragments of DNA that can copy themselves and integrate into different parts of the genome ­ can greatly disrupt the integrity of the germ cell genome. Systems involving small RNAs and DNA methylation, which respectively modify the sequence and structure of the genome, can protect germ cells from the activity of transposable elements. While these systems have been studied extensively in late germ cells, less is known about how they work in germ cells generated early on in development. To investigate, Pang et al. studied the germline stem cells that give rise to eggs in female fruit flies. Techniques that measure DNA modifications showed that these germline stem cells and the cells they give rise to early on are better protected against transposable elements. This is likely due to the unusual cell cycle of early germ cells, which display a very short initial growth phase and special DNA replication timing during the synthesis phase. Until now, the purpose of these long-known cell cycle differences between early and late germ cells was not understood. Experiments also showed known transposable element defences are upregulated before the cell division that produces reproductive cells. DNA becomes more densely packed and germ cells connect with one another, forming germline 'cysts' that allow them to share small RNAs that can suppress transposable elements. Pang et al. propose that these changes compensate for the loss of enhanced repression that occurs in the earlier stem cell stage. Very similar changes also take place in the cells generated from fertilized eggs and in mammalian reproductive cells. Further experiments investigated how these changes impact the transition from stem cell to egg cell, revealing that germline stem cells express a wide diversity of genes, including most genes whose transcripts will be stored in the mature egg later on. Another type of cell produced by germline stem cells known as nurse cells, which synthesize most of the contents of the egg, dramatically upregulate genes supporting growth. Meanwhile, 25% of genes initially expressed in germline stem cells are switched off during the transition, partly due to a mechanism called Polycomb-mediated repression. The findings advance fundamental knowledge of how germline stem cells become egg cells, and could lead to important findings in developmental biology. Furthermore, understanding that for practical applications germline stem cells do not need to retain transposable element controls designed for evolutionary time scales means that removing them may make it easier to obtain and manipulate new stem cell lines and to develop new medical therapies.

A symbiotic physical niche in Drosophila melanogaster regulates stable association of a multi-species gut microbiota.

The gut is continuously invaded by diverse bacteria from the diet and the environment, yet microbiome composition is relatively stable over time for host species ranging from mammals to insects, suggesting host-specific factors may selectively maintain key species of bacteria. To investigate host specificity, we used gnotobiotic Drosophila, microbial pulse-chase protocols, and microscopy to investigate the stability of different strains of bacteria in the fly gut. We show that a host-constructed physical niche in the foregut selectively binds bacteria with strain-level specificity, stabilizing their colonization. Primary colonizers saturate the niche and exclude secondary colonizers of the same strain, but initial colonization by Lactobacillus species physically remodels the niche through production of a glycan-rich secretion to favor secondary colonization by unrelated commensals in the Acetobacter genus. Our results provide a mechanistic framework for understanding the establishment and stability of a multi-species intestinal microbiome.