Department of Preventive and Community Dentistry, School of Dentistry, Federal University of Rio Grande do Sul, Porto Alegre, Brazil.
School of Dentistry, University of Leeds, Leeds, United Kingdom.
Caries Res. 2022;56(2):116-128. doi: 10.1159/000524196. Epub 2022 Apr 1.
The literature is still scarce on studies describing Streptococcus mutans global gene expression under clinical conditions such as those found on complex biofilms from sound root surfaces (SRS) and carious root surfaces (RC). This study aimed to investigate the S. mutans gene expression and functional profile within the metatranscriptome of biofilms from SRS and from RC in an attempt to identify enriched functional signatures potentially associated with the healthy-to-disease transitioning process. Total RNA was extracted, and prepared libraries (SRS = 10 and RC = 9) were paired-end sequenced using the Illumina HiSeq2500. A read count assigned to each gene of the S. mutans UA159 strain was obtained. Differentially expressed genes (DEG) between SRS and RC were identified using the DESeq2 R package, and weighted gene co-expression network analysis (WGCNA) was performed to explore and identify functional modules related to SRS and RC. We found seventeen DEG between SRS and RC samples, with three overexpressed in RC and related to membrane protein, alanyl-tRNA synthetase, and GTP-binding protein, with the remaining ones overexpressed in SRS samples and related to hypothetical protein, transposon integrase, histidine kinase, putative transporter, bacteriocin immunity protein, response regulator, 6-phospho-beta-galactosidase, purine metabolism, and transcriptional regulator. Key-functional modules were identified for SRS and RC conditions based on WGCNA, being 139 hub genes found on SRS key-module and 17 genes on RC key-module. Functional analysis of S. mutans within the metatranscriptome of biofilms from sound root and from carious root revealed a similar pattern of gene expression, and only a few genes have been differentially expressed between biofilms from SRS and those from root carious lesions. However, S. mutans presented a greater functional abundance in the carious lesion samples. Some functional patterns related to sugar (starch, sucrose, fructose, mannose, and lactose) and heterofermentative metabolisms, to cell-wall biosynthesis, and to acid tolerance stress seem to be enriched on carious root surfaces, conferring ecological advantages to S. mutans. Altogether, the present data suggest that a functional signature may be associated with carious root lesions.
关于变形链球菌在临床条件下（如完整根面和龋坏根面的复杂生物膜）的全基因表达的研究文献仍然较少。本研究旨在通过对完整根面和龋坏根面生物膜的宏转录组进行分析，调查变形链球菌的基因表达和功能谱，试图鉴定与健康到疾病转变过程相关的丰富功能特征。提取总 RNA，制备文库（SRS=10 个，RC=9 个），并使用 Illumina HiSeq2500 进行 PE 测序。获得 S. mutans UA159 菌株每个基因的读数计数。使用 DESeq2 R 包鉴定 SRS 和 RC 之间差异表达基因（DEG），并进行加权基因共表达网络分析（WGCNA），以探索和鉴定与 SRS 和 RC 相关的功能模块。我们在 SRS 和 RC 样本之间发现了 17 个 DEG，其中 3 个在 RC 中过表达，与膜蛋白、丙氨酰-tRNA 合成酶和 GTP 结合蛋白有关，其余的在 SRS 样本中过表达，与假设蛋白、转座子整合酶、组氨酸激酶、假定转运蛋白、细菌素免疫蛋白、应答调节蛋白、6-磷酸-β-半乳糖苷酶、嘌呤代谢和转录调节因子有关。基于 WGCNA，确定了 SRS 和 RC 条件下的关键功能模块，在 SRS 关键模块中发现了 139 个枢纽基因，在 RC 关键模块中发现了 17 个基因。对完整根面和龋坏根面生物膜宏转录组中的变形链球菌进行功能分析，发现基因表达模式相似，仅在完整根面和龋坏根面生物膜之间有少数基因存在差异表达。然而，变形链球菌在龋坏病变样本中的功能丰度更高。一些与糖（淀粉、蔗糖、果糖、甘露糖和乳糖）和异型发酵代谢、细胞壁生物合成和耐酸应激相关的功能模式似乎在龋坏根面富集，为变形链球菌提供了生态优势。总的来说，本研究数据表明，一种功能特征可能与龋坏根面病变有关。
