Comparative RNA-Seq data for L. interrogans sv. Manilae L495 wild-type and perRA/B strains cultivated in dialysis membrane chambers (DMCs).

The genome sequence of L. interrogans sv. Manilae strain UP-MMC-NIID LP (accession numbers NZ_CP011931.1, NZ_CP011932.1 and NZ_CP011933.1) was used for mapping and differential gene expression analysis. All non-coding RNAs and pseudogenes were removed before DESeq2 analysis. Column A: RefSeq locus tag. Column B: Locus tag. Column C: L. interrogans sv. Copenhageni strain Fiocruz L1-130 (accession numbers NC_005823.1 and NC_005824.1) orthologs identified using OrthoVenn 2.0. [202]. Dashes (-) indicate genes for which no clear ortholog was identified. Column D: Description of gene product, following genome annotation. Column E. Identification of conserved domain(s) within the corresponding gene product based on search of the Interpro database [190, 201]. The domain identification for each gene is followed by description; [D] indicates a domain; [F] indicates a protein family; [H] indicates a homologous superfamily. Column F. Uniprot entry for the orthologous gene in L. interrogans sv. Copenhageni strain Fiocruz L1-130 genome. Columns G, H: Clusters of Orthologous Group (COG) classifications based on MicroScope [187]. Column I: Regulation of the corresponding gene based on RNA-Seq analysis by Zavala-Alvarado et al. [93, 94] performed using the same strains cultivated in vitro. Positive and negative numbers indicate upregulation and repression, respectively, in the WT compared to mutant strain. Dashes (-) indicate genes that are not differentially regulated at least 3-fold (p≤0.05) by PerRA/B in vitro. Column J: Fold-regulation determined using DESeq2 based on WT vs. the perRA/B double mutant RNA-Seq analysis using leptospires cultivated within DMCs. Column K: Type of regulation by PerRA/B in DMCs. Genes expressed at ≥3-fold higher/lower levels in the WT versus mutant with a False-discovery rate-adjusted-p value (q) ≤0.05 were considered differentially expressed. “NO” indicates genes that are not regulated by PerRA/B in DMCs; “Up” indicates genes upregulated by PerRA/B in DMCs (expressed at lower levels in the mutant vs. WT); “Down” indicates genes downregulated by PerRA/B in DMCs (expressed at higher levels in the mutant vs. WT). Column L: Behavior of the corresponding gene in the WT vs. perRA (A) and perRB (B) mutants by RNA-Seq using L. interrogans cultivated in DMCs. “Up” and “Down”, respectively, are used to significant (≥3-fold, q≤0.05) upregulation or repression of the gene in the WT compared to the mutant. Columns M-R: Number of mapped reads per gene for each one of the three biological replicates per strain. Columns S-AF: Output from DESeq2 for WT vs. perRA/B mutant strains cultivated in DMCs (3 biological replicates per strain). Column S: Mean DESeq2 values for each gene. Column T: Log2 fold change in gene expression. Column U: Power function transformation of Log2 fold change. Column V: Fold regulation. Column W-Z. Statistical analysis of differential gene expression including standard error estimate for the log2 fold change estimate (lfcSE, column T) and adjusted p-value (W). Columns AA-AF: Normalized copy numbers per gene (3 biological replicates per strain). (XLSX)