Fungal Divergent Actin: Trait mapping and function hypothesis

This projects investigates the potential new function of a divergent actin form mainly found in fungal species (Fungal Divergent Actin (FDA)) using trait mapping and association analysis as a novel strategy to generate hypotheses about protein function. We use the ProteinCartography pipeline (https://doi.org/10.57844/arcadia-a5a6-1068), combined with trait mapping and trait association analysis to generate hypotheses about the function of FDA. The overall idea is to identify a working set of fungal species for which we are able to confidently determine the presence or absence of fungal divergent actin, gather fungal trait information for these species (ecological traits, structural traits, genetic traits etc...) and determine whether there is any correlation between the presence/absence of FDA and one of the fungal trait. Any correlation between FDA presence/absence and fungal trait can then be used to infer hypothesis about the function of FDA. Our approach is divided into four main steps: - Step 1: Expanding the initial set of fungal species that possess FDA - Step 2: Defining the 'working set of species' (set of fungal species for which we can determine their FDA status (presence or absence)) - Step 3: Curating fungal trait information - Step 4: Statistical modeling of the association of FDA and chosen fungal traits In this upload, we provide files that are parts of Steps 1 & 2: - ProteinCartography folder of the ProteinCartography run for the FDA proteins: fungal_divergent_actins_PC.zip - .csv table of all fungal proteins and associated species in Uniprot that have available structure in AlphaFold: Fungi_prot_uniprot.csv ProteinCartography run: fungal_divergent_actins_PC.zip (Step 1 - Expanding the initial set of fungal species that possess FDA) The aim of the first step, is to detect as many fungal species as possible that possess FDA. For this, we used ProteinCartography (https://doi.org/10.57844/arcadia-a5a6-1068), to screen for protein that have similar structures than the previously identified Fungal Divergent Actin (REF actin pub) and expand the original cluster of FDA. After identifying 6 representative sequences of Fungal Divergent Actins, we used each of the six proteins as input proteins for "Search Mode'' of the pipeline ProteinCartography. Full details on the ProteinCartography pipeline can be found in the GitHub repository and accompanying pub (https://doi.org/10.57844/arcadia-a5a6-1068). The fungal_divergent_actins_PC.zip contains all the inputs and outputs of the ProteinCartography run: fasta and pdb files for all 6 input proteins configuration file for the ProteinCatography run all output files (including main files presented in the Pub: similarity matrix, semantic analysis and aggregated_features_pca_umap in the subfolder output/clusteringresults Uniprot list of fungal protein with available structure: Fungi_prot_uniprot.csv (Step 2 - Defining the 'working set of species') The aim of Step 2 is to identify the list of fungal species for which we can confidently determine the FDA presence/absence status. While ProteinCartography allows us to identify species that possess FDA, we also need to be able to confidently tell when a species doesn't possess FDA. Thus, the working set is defined as the set of species for which the presence or absence of FDA was putatively established. Because ProteinCartography relies on protein structures available in UniProt and AlphaFold, we decided to define our working set as any fungal species that has a minimum of 6000 protein structures in AlphaFold. Then we consider that any species of this set that is not part of the extended cluster does not possess FDA. Fungi_prot_uniprot.csv is the list of fungal proteins and associated species that have structure avaialable in AlphaFold from UniProt. This serves as the initial file to eventually count the number of proteins with available structures per species and identify the working set of fungal species - To obtain this list we conducted an 'Advanced search' in UniProt using the following query: 'Fungi' in Taxonomy field ' * ' for the field AlphaFoldDB cross-reference (found within the Cross reference /3D structure field)本项目以性状定位与关联分析作为全新的蛋白质功能假说生成策略，探究主要存在于真菌类群中的一类真菌异型肌动蛋白（Fungal Divergent Actin, FDA）的潜在新功能。我们结合ProteinCartography流程（https://doi.org/10.57844/arcadia-a5a6-1068）与性状定位、性状关联分析，为FDA的功能生成研究假说。 本研究的核心思路为：筛选出可确定性判定FDA存在与否的真菌物种工作集，收集这些物种的性状信息（包括生态性状、结构性状、遗传性状等），并分析FDA的存在状态与真菌性状之间是否存在相关性。后续可依托FDA存在与否与真菌性状间的关联，推导得到关于FDA功能的研究假说。 本研究方法分为四个主要步骤： - 步骤1：拓展初始携带FDA的真菌物种集 - 步骤2：定义「真菌物种工作集」（即可确定性判定FDA存在/缺失状态的真菌物种集合） - 步骤3：整理真菌性状信息 - 步骤4：构建FDA与选定真菌性状间关联的统计模型 本次上传的文件属于步骤1与步骤2的相关内容： - 针对FDA蛋白的ProteinCartography流程运行结果文件夹：fungal_divergent_actins_PC.zip - 收录通用蛋白质资源库（UniProt）中所有带有阿尔法折叠（AlphaFold）可用结构的真菌蛋白及对应物种的.csv表格：Fungi_prot_uniprot.csv ### ProteinCartography流程运行结果包：fungal_divergent_actins_PC.zip（对应步骤1：拓展初始携带FDA的真菌物种集） 步骤1的目标为尽可能多地筛选出携带FDA的真菌物种。为此，我们借助ProteinCartography流程（https://doi.org/10.57844/arcadia-a5a6-1068），检索与此前鉴定得到的真菌异型肌动蛋白（参考文献中的靶标肌动蛋白）结构相似的蛋白，以此拓展FDA的初始聚类簇。 我们首先鉴定得到6条真菌异型肌动蛋白的代表性序列，随后将这6个蛋白分别作为输入蛋白，提交至ProteinCartography流程的「搜索模式」。关于ProteinCartography流程的完整细节，可查阅其GitHub仓库及配套发表论文（https://doi.org/10.57844/arcadia-a5a6-1068）。 fungal_divergent_actins_PC.zip包含本次ProteinCartography运行的全部输入与输出文件： 1. 6条输入蛋白的fasta与pdb文件 2. ProteinCartography流程运行的配置文件 3. 全部输出文件（包括论文中展示的核心文件：相似性矩阵、语义分析结果，以及子文件夹output/clusteringresults中的aggregated_features_pca_umap文件） ### 带有阿尔法折叠（AlphaFold）可用结构的真菌蛋白UniProt列表：Fungi_prot_uniprot.csv（对应步骤2：定义真菌物种工作集） 步骤2的目标为确定可确定性判定FDA存在/缺失状态的真菌物种列表。尽管ProteinCartography可帮助我们鉴定携带FDA的物种，但我们同时需要可靠判定哪些物种不携带FDA。因此，本工作集被定义为可确定性确立FDA存在与否的物种集合。 由于ProteinCartography依赖UniProt与AlphaFold数据库中可用的蛋白结构，我们将工作集设定为：AlphaFold数据库中至少包含6000条蛋白结构的真菌物种。随后，我们认为该工作集中未被纳入拓展后FDA聚类簇的物种，均不携带FDA。 Fungi_prot_uniprot.csv是收录了UniProt中所有带有AlphaFold可用结构的真菌蛋白及对应物种的列表，可作为初始文件统计各物种的可用结构蛋白数量，并最终确定真菌物种工作集。 该列表通过在UniProt中执行高级检索得到，检索条件如下： - 分类学字段限定为「Fungi」 - AlphaFoldDB交叉引用字段（位于交叉引用/3D结构子字段中）为「*」，即匹配所有条目