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

Boggiatto, Paola M.; Fitzsimmons, Daniel; Bayles, Darrell O.; Alt, David; Vrentas, Catherine E.; Olsen, Steven C.

doi:10.1186/s12867-018-0111-x

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

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

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ISSN: 1471-2199

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