bioRxiv Science⌕ Search

Biology subjects

Nakayasu, E.

Publications and source records attributed to Nakayasu, E..

4 recordsLinked to original sources

Efficient genetic code expansion tools enable in vivo study of lysine acetylation in non-model bacteria

Recent proteomic advancements have revealed widespread N{varepsilon}-lysine acetylation in pathways governing pathogenicity, metabolism, and antibiotic resistance in bacteria. The spontaneous, non-specific nature of this modification in prokaryotes obscures its biological role, necessitating prokaryotic specific in vivo interrogation systems. Genetic Code Expansion (GCE) offers a powerful method to investigate the roles and regulation dynamics of acetyl-lysine in vivo with the precise incorporation of a suite of non-canonical amino acids, including acetyl-lysine analogs. However, its use has been largely restricted to E. coli strains due to challenges associated with implementation and optimization of the technology in more diverse bacterial strains. Here, we present a bacterial host-agnostic, readily optimizable GCE platform designed to site-specifically incorporate non-canonical amino acids into target proteins within living bacteria. We further demonstrate the versatility of this technology by showcasing, for the first time, the successful incorporation of acetyl-lysine in a non-E. coli bacterium.

synthetic biology↗

Reduction of chemokine CXCL9 expression by omega-3 fatty acids via ADP-ribosylhydrolase ARH3 in MIN6 insulin-producing cells

Type 1 diabetes (T1D) results from the autoimmune destruction of the insulin producing {beta} cells of the pancreas. Omega-3 fatty acids protect {beta} cells and reduce the incident of T1D. However, how omega-3 fatty acids act on {beta} cells is not well understood. We have shown that omega-3 fatty acids reduce pro-inflammatory cytokine-mediated {beta}-cell apoptosis by upregulating the expression of the ADP-ribosylhydrolase ARH3. Here, we further investigate the {beta}-cell protection mechanism by ARH3 by performing siRNA of its gene Adprhl2 in MIN6 insulin-producing cells followed by treatment with a cocktail of the pro-inflammatory cytokines IL-1{beta} + IFN-{gamma} + TNF-, and proteomics analysis. ARH3 regulated proteins from several pathways related to the nucleus (splicing, RNA surveillance and nucleocytoplasmic transport), mitochondria (metabolic pathways) and endoplasmic reticulum (protein folding). ARH3 also regulated the levels of cytokine-signaling proteins related to the antigen processing and presentation, and chemokine-signaling pathway. We further studied the role of ARH in regulating the chemokine CXCL9. We confirmed that ARH3 reduces the cytokine-induced expression of CXCL9 by ELISA. We also found that CXCL9 expression is regulated by omega-3 fatty acids. In conclusion, we showed that omega-3 fatty acids regulate CXCL9 expression via ARH3, which might have a role in protecting {beta} cells from immune attack and preventing T1D development.

cell biology↗

The impact of pro-inflammatory cytokines on the β-cell regulatory landscape provides new insights into the genetics of type 1 diabetes

Early stages of type 1 diabetes (T1D) are characterized by local autoimmune inflammation and progressive loss of insulin-producing pancreatic {beta} cells. We show here that exposure to pro-inflammatory cytokines unmasks a marked plasticity of the {beta}-cell regulatory landscape. We expand the repertoire of human islet regulatory elements by mapping stimulus-responsive enhancers linked to changes in the {beta}-cell transcriptome, proteome and 3D chromatin structure. Our data indicates that the {beta} cell response to cytokines is mediated by the induction of novel regulatory regions as well as the activation of primed regulatory elements pre-bound by islet-specific transcription factors. We found that T1D-associated loci are enriched of the newly mapped cis-regulatory regions and identify T1D-associated variants disrupting cytokine-responsive enhancer activity in human {beta} cells. Our study illustrates how {beta} cells respond to a pro-inflammatory environment and implicate a role for stimulus-response islet enhancers in T1D.

genomics↗

Cryptococcus neoformans secretes small molecules that inhibit IL-1β inflammasome-dependent secretion

Cryptococcus neoformans is an encapsulated yeast that causes disease mainly in immunosuppressed hosts. It is considered a facultative intracellular pathogen because of its capacity to survive and replicate inside phagocytes, especially macrophages. This capacity is heavily dependent on various virulence factors, particularly the glucuronoxylomannan (GXM) component of the polysaccharide capsule, that render the non- or poorly-activated macrophage ineffective against phagocytosed yeast. Strategies utilized by macrophages to prevent this scenario include pyroptosis (a rapid highly inflammatory cell death) and vomocytosis (the expulsion of the pathogen from the intracellular environment without lysis). Inflammasome activation in phagocytes is usually protective against fungal infections, including cryptococcosis. Nevertheless, recognition of C. neoformans by inflammasome receptors requires specific changes in morphology or the opsonization of the yeast, impairing a proper inflammasome function. In this context, we analyzed the impact of molecules secreted by C. neoformans B3501 strain and its acapsular mutant{Delta} cap67 in an inflammasome activation in vitro model. Our results showed that conditioned media derived from B3501 was capable of inhibiting inflammasome dependent events (i. e. IL-1{beta} secretion and LDH release via pyroptosis) more strongly than conditioned media from{Delta} cap67, regardless of GXM presence. We also demonstrated that macrophages treated with conditioned media were less responsive against infection with the virulent strain H99, exhibiting lower rates of phagocytosis, increased fungal burdens and enhanced vomocytosis. Moreover, we showed that the aromatic metabolite DL-Indole-3-lactic acid (ILA) was present in B3501s conditioned media and that this fungal metabolite is involved in the regulation of inflammasome activation by C. neoformans. Overall, the results presented show that conditioned media from a wild-type strain can inhibit an important recognition pathway and subsequent fungicidal functions of macrophages, contributing to fungal survival in vitro and suggesting that this serves as an important role for secreted molecules during cryptococcal infections. Authors SummaryCryptococcus neoformans is the agent of cryptococcal meningitis, a disease that can be life-threatening in immunocompromised hosts such as those infected with HIV. The infection thrives in hosts that poorly activate their immune system, mainly because of the yeasts ability to survive inside macrophages and migrate towards the central nervous system. Emerging data indicate that cryptococci modulate the host immune response, but the underlying mechanisms remain largely uncharacterized. Here we show that secreted molecules from a wild-type strain of C. neoformans impair inflammatory responses driven by inflammasome activation, which in turn impact the macrophage antifungal activity. We further show that this inhibition does not involve GXM, the main constituent of the fungal capsule, but rather is partially dependent on DL-Indole-3-lactic acid (ILA), a metabolite not previously implicated in fungal virulence.

immunology↗