Section for Genome Biology, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås NO-1432, Norway.
Department of Chemistry, Biotechnology and Food Science (IKBM), Norwegian University of Life Sciences, Ås NO-1432, Norway.
G3 (Bethesda). 2023 Jun 1;13(6). doi: 10.1093/g3journal/jkad069.
Chitin is one of the most abundant polysaccharides in nature, forming important structures in insects, crustaceans, and fungal cell walls. Vertebrates on the other hand are generally considered "nonchitinous" organisms, despite having highly conserved chitin metabolism-associated genes. Recent work has revealed that the largest group of vertebrates, the teleosts, have the potential to both synthesize and degrade endogenous chitin. Yet, little is known about the genes and proteins responsible for these dynamic processes. Here, we used comparative genomics, transcriptomics, and chromatin accessibility data to characterize the repertoire, evolution, and regulation of genes involved in chitin metabolism in teleosts, with a particular focus on Atlantic salmon. Reconstruction of gene family phylogenies provides evidence for an expansion of teleost and salmonid chitinase and chitin synthase genes after multiple whole-genome duplications. Analyses of multi-tissue gene expression data demonstrated a strong bias of gastrointestinal tract expression for chitin metabolism genes, but with different spatial and temporal tissue specificities. Finally, we integrated transcriptomes from a developmental time series of the gastrointestinal tract with chromatin accessibility data to identify putative transcription factors responsible for regulating chitin metabolism gene expression (CDX1 and CDX2) as well as tissue-specific divergence in the regulation of gene duplicates (FOXJ2). The findings presented here support the hypothesis that chitin metabolism genes in teleosts play a role in developing and maintaining a chitin-based barrier in the teleost gut and provide a basis for further investigations into the molecular basis of this barrier.
几丁质是自然界中最丰富的多糖之一，构成昆虫、甲壳类动物和真菌细胞壁的重要结构。另一方面，脊椎动物通常被认为是“无几丁质”的生物体，尽管它们具有高度保守的几丁质代谢相关基因。最近的研究表明，最大的脊椎动物群体——硬骨鱼，具有合成和降解内源性几丁质的潜力。然而，对于负责这些动态过程的基因和蛋白质，人们知之甚少。在这里，我们使用比较基因组学、转录组学和染色质可及性数据来描述硬骨鱼中参与几丁质代谢的基因的组成、进化和调控，特别关注大西洋鲑鱼。基因家族系统发育重建的证据表明，在多次全基因组复制后，硬骨鱼和鲑鱼的几丁质酶和几丁质合成酶基因发生了扩张。多组织基因表达数据分析表明，胃肠道对几丁质代谢基因的表达具有强烈的偏倚，但具有不同的时空组织特异性。最后，我们将胃肠道发育时间序列的转录组与染色质可及性数据整合，以鉴定负责调节几丁质代谢基因表达的潜在转录因子（CDX1 和 CDX2），以及基因重复调控的组织特异性差异（FOXJ2）。这里提出的发现支持了这样的假设，即硬骨鱼中的几丁质代谢基因在硬骨鱼肠道中形成和维持基于几丁质的屏障中发挥作用，并为进一步研究这种屏障的分子基础提供了基础。
