McKinnie Lachlan J, Cummins Scott F, Zhao Min
Seaweed Research Group, University of the Sunshine Coast, Maroochydore, QSL 4558, Australia.
School of Science, Technology, and Engineering, University of the Sunshine Coast, Maroochydore, QSL 4558, Australia.
Mar Drugs. 2023 Dec 19;22(1):3. doi: 10.3390/md22010003.
Rhodophytes (red algae) are an important source of natural products and are, therefore, a current research focus in terms of metabolite production. The recent increase in publicly available Rhodophyte whole genome and transcriptome assemblies provides the resources needed for in silico metabolic pathway analysis. Thus, this study aimed to create a Rhodophyte multi-omics resource, utilising both genomes and transcriptome assemblies with functional annotations to explore Rhodophyte metabolism. The genomes and transcriptomes of 72 Rhodophytes were functionally annotated and integrated with metabolic reconstruction and phylogenetic inference, orthology prediction, and gene duplication analysis to analyse their metabolic pathways. This resource was utilised via two main investigations: the identification of bioactive sterol biosynthesis pathways and the evolutionary analysis of gene duplications for known enzymes. We report that sterol pathways, including campesterol, β-sitosterol, ergocalciferol and cholesterol biosynthesis pathways, all showed incomplete annotated pathways across all Rhodophytes despite prior in vivo studies showing otherwise. Gene duplication analysis revealed high rates of duplication of halide-associated haem peroxidases in Florideophyte algae, which are involved in the biosynthesis of drug-related halogenated secondary metabolites. In summary, this research revealed trends in Rhodophyte metabolic pathways that have been under-researched and require further functional analysis. Furthermore, the high duplication of haem peroxidases and other peroxidase enzymes offers insight into the potential drug development of Rhodophyte halogenated secondary metabolites.
红藻是天然产物的重要来源，因此，就代谢产物生产而言，是当前的研究重点。最近公开的红藻全基因组和转录组组装数据的增加，为计算机代谢途径分析提供了所需的资源。因此，本研究旨在创建一个红藻多组学资源，利用带有功能注释的基因组和转录组组装数据来探索红藻的代谢。对72种红藻的基因组和转录组进行功能注释，并与代谢重建、系统发育推断、直系同源预测和基因重复分析相结合，以分析它们的代谢途径。通过两项主要研究利用了这一资源：生物活性甾醇生物合成途径的鉴定以及已知酶基因重复的进化分析。我们报告称，尽管先前的体内研究有不同结果，但包括菜油甾醇、β-谷甾醇、麦角钙化醇和胆固醇生物合成途径在内的甾醇途径，在所有红藻中均显示注释不完整的途径。基因重复分析显示，在红藻纲藻类中，与卤化物相关的血红素过氧化物酶的重复率很高，这些酶参与与药物相关的卤化次生代谢产物的生物合成。总之，本研究揭示了红藻代谢途径中尚未充分研究且需要进一步功能分析的趋势。此外，血红素过氧化物酶和其他过氧化物酶的高重复率为红藻卤化次生代谢产物的潜在药物开发提供了见解。
