Cromie Gareth A, Tan Zhihao, Hays Michelle, Sirr Amy, Dudley Aimée M
Pacific Northwest Research Institute, Seattle, Washington, United States of America.
Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, United States of America.
PLoS One. 2024 Dec 5;19(12):e0311061. doi: 10.1371/journal.pone.0311061. eCollection 2024.
Clonal communities of single celled organisms, such as bacterial or fungal colonies and biofilms, are spatially structured, with subdomains of cells experiencing differing environmental conditions. In the development of such communities, cell specialization is not only important to respond and adapt to the local environment but has the potential to increase the fitness of the clonal community through division of labor. Here, we examine colony development in a yeast strain (F13) that produces colonies with a highly structured "ruffled" phenotype in the colony periphery and an unstructured "smooth" phenotype in the colony center. We demonstrate that in the F13 genetic background deletions of transcription factors can either increase (dig1D, sfl1D) or decrease (tec1D) the degree of colony structure. To investigate the development of colony structure, we carried out gene expression analysis on F13 and the three deletion strains using RNA-seq. Samples were taken early in colony growth (day2), which precedes ruffled phenotype development in F13, and from the peripheral and central regions of colonies later in development (day5), at which time these regions are structured and unstructured (respectively) in F13. We identify genes responding additively and non-additively to the genotype and spatiotemporal factors and cluster these genes into a number of different expression patterns. We identify clusters whose expression correlates closely with the degree of colony structure in each sample and include genes with known roles in the development of colony structure. Individual deletion of 26 genes sampled from different clusters identified 5 with strong effects on colony morphology (BUD8, CIS3, FLO11, MSB2 and SFG1), all of which eliminated or greatly reduced the structure of the F13 outer region.
单细胞生物的克隆群落，如细菌或真菌菌落及生物膜，具有空间结构，其中细胞亚域经历不同的环境条件。在这类群落的发育过程中，细胞特化不仅对于响应和适应局部环境很重要，而且有可能通过分工提高克隆群落的适应性。在此，我们研究了一种酵母菌株（F13）的菌落发育情况，该菌株产生的菌落在菌落周边具有高度结构化的“褶皱”表型，而在菌落中心具有非结构化的“光滑”表型。我们证明，在F13遗传背景下，转录因子的缺失可以增加（dig1D、sfl1D）或降低（tec1D）菌落结构的程度。为了研究菌落结构的发育，我们使用RNA测序对F13和三种缺失菌株进行了基因表达分析。在菌落生长早期（第2天）取样，此时F13的褶皱表型尚未发育，在发育后期（第5天）从菌落的周边和中心区域取样，此时这些区域在F13中分别为结构化和非结构化。我们鉴定了对基因型和时空因素呈累加性和非累加性响应的基因，并将这些基因聚类为多种不同的表达模式。我们鉴定出其表达与每个样本中菌落结构程度密切相关的聚类，并包括在菌落结构发育中具有已知作用的基因。从不同聚类中选取的26个基因的单个缺失鉴定出5个对菌落形态有强烈影响的基因（BUD8、CIS3、FLO11、MSB2和SFG1），所有这些基因都消除或大大降低了F13外部区域的结构。
