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Table 3 Candidate genes of interest based on abundance in long-term Brucella samples

From: Coincidence cloning recovery of Brucella melitensis RNA from goat tissues: advancing the in vivo analysis of pathogen gene expression in brucellosis

Locus tag Product name/description Rank in acidified culture [52] Rank in long-term Log2Expn in LT vs. culture Growth phase reg. [53] Reg. in cattle (4 h) [27] Reg. in MΦ (24 h) [54]
BMEI0050 CobT (Cobalamin biosynthesis) 2043 41 2.7 N Mixed effects No change
BMEI0460 MoxR family protein 1892 42 3.1 N Repressed Slight repress
BMEI0461 Hypothetical protein 1971 31 3.1 N No change Slight repress
BMEI0828 Phosphatidate cytidyltransferase 2101 95 5.9 N Activated Slight repress
BMEI1817 ATP-dependent helicase HrpB 3100 1291 6.6 N Repressed No change
BMEI1896 Hypothetical protein 2953 17 2.8 N Repressed No change
BMEII0111 ICC protein family 2227 136 3.2 N Activated No change
BMEII0113 sn-Glycerol-3-phosphate transport system UgpA 3026 94 3.2 N Repressed No change
BMEII0114 sn-Glycerol-3-phosphate transport system UgpE 2611 254 2.9 Y Repressed No change
BMEII0167 FlhA2 flagellar biosynthesis protein 2902 71 2.9 N Repressed No change
BMEII0831 Hypothetical protein 1937 253 7.7 N Activated No change
BMEII0832 UDP-glucose-4-epimerase 3128 239 7.5 N Repressed No change
  1. Relevant expression information for each gene candidate is compiled from external data sources as described, plus the coincidence cloning data set presented in this paper. Rank in acidified culture: Rank of gene in Liu et al. [52] expression set, sorted from high (1) to low (3152) by RPKM. Rank in long-term: Rank of gene in averaged long-term expression set from coincidence cloning (CC), sorted from high (1) to low (3264) by gene expression normalized to gene and library size in SeqMonk (FPKM). Log2Expn: log2 (expression in long-term samples/expression in culture-derived samples) for CC dataset, generated as log2 (FPM for long-term/FPM for culture) in SeqMonk. Growth phase reg: Expresses whether (yes/no) the gene locus was identified as exhibiting a significant and > 2-fold change in gene expression between log and stationary phase in culture by Rossetti et al. [53]. Reg. in cattle: describes pattern of gene expression observed over the first 4 h. of introduction of cultured B. melitensis to cattle intestinal sections [27]. Reg. in macrophages: Describes pattern of gene expression observed 24 h post-murine macrophage infection, as compared to expression pre-infection in broth culture [54]. Data from Liu et al. [52] reflect actively growing cultures in vitro in Tryptic Soy Broth (fresh media added after subculture from stationary phase), exposed to acid stress like that expected in a macrophage (pH 3.4). Data from the culture-derived coincidence cloning (CC) samples was obtained from parallel CC of RNA derived from overnight cultures of the B. melitensis 16M challenge strain grown in Brucella broth