Table 2 Gene targets and q-PCR primers used in this study with their derived proteins and functional classification. References include previous studies in which the target gene was investigated, chlamydial species studied and the model of persistence: PenG: penicillin; ID: iron depletion; IFN-γ, HS: Heat shock
Gene | Primer sequence (5′-3′) | Protein | Functional classification | Reference |
|---|---|---|---|---|
16S rRNA | Fw: CTTGTACACACCGCCCGTC Rv: GCCCAACCTAGTCAAACCGTC | Ribosomal RNA | Reference gene | |
GroEL | Fw: CAACAGGTAGCAGAATCCGGA Rv: CTCTTCGCTGATCAATTGGCCA | Heat shock protein 60 | Stress response | Kalmar et al., 2015 [42] C. abortus and C. psittaci |
dnaK | Fw: ACCAACCGTTCATCACTATGGA Rv: TGGCATGGAGCTTTTGTACG | Heat shock protein 70 | Mukhopadhyay et al., 2006 [43] C. pneumoniae. ID, IFN-γ, HS. | |
htrA | Fw: CAAGATGACGGTGTCTCTGCTTT Rv: TGCTTCGACAGAAACAATCAGCA | Protease | Timms et al., 2009 [17] C. pneumoniae. IFN-γ, ID | |
grpE | Fw: CAACAGTTCCTACCCCCGATAA Rv: CCTCATCTGACATCTGTGAGGC | Cofactor Hsp70 | Goellner et al., 2006 [15] C. psittaci. PenG, ID, IFN-γ | |
ompA | Fw: GCATTATTGTTTGCCGCTAC Rv: ATCACCTGAAGCACCTTCCCA | MOMP | Membrane proteins | Timms et al., 2009 [17] C. pneumoniae. IFN-γ, ID |
omcA | Fw: TGCCGTATTGTAGATTGCTGCT Rv: TGAACTCCTGAATTGCACTCAG | outer mb protein A | Goellner et al., 2006 [15] C. psittaci. PenG, ID, IFN-γ | |
omcB | Fw: GTCGTATTCGATGCTCTGCCTA Rv: AGCAACGGGTACCGTTAAAGT | outer mb complex protein B | Amirshahi et al., 2011 [22] C. trachomatis. Estradiol and progesterone | |
pmp17G | Fw: GGGTGATTGGGGTAACGATTGT Rv: AGGTTGGTGAGATTGCTGCT | Polymorphic mb protein | Wheelhouse et al., 2009 [36] C. abortus | |
ftsW | Fw: TTGTTCCCTGCGTCGCTATC Rv: AAAAGCTATTACGGCTGCGGA | cell division mb protein | Cell division | Kalmar et al., 2015 [42] C. abortus and C. psittaci |
hctA | Fw: ACGTGACTTAGACAAGGCCGA Rv: TGCTTTACGCTTAGATGCTGATT | DNA-binding histone-like protein | Regulation of RB-to-EB conversion | Goellner et al., 2006 [15] C. psittaci. PenG, ID, IFN-γ |
euo | Fw: AAGGCTTCTAAAACAACCCGG Rv: GGCTAATAACCCAAGCAGCG | DNA binding protein | Goellner et al., 2006 [15] C. psittaci. PenG, ID, IFN-γ | |
Cpaf | Fw: CGCACCCTGAGCATCGTTA Rv: AAGACAAAACCCCCAGCTCCT | chlamydial protease-like activity factor | Degradation of proteins | Kalmar et al., 2015 [42] C. abortus and C. psittaci |
sctN | Fw: TTCGATACCCTCATGTCGCAA Rv: TACCTCCCCAACGCGTACATT | type III secretion cytoplasmic ATPase | Type III secretion system | Goellner et al., 2006 [15] C. psittaci. PenG, ID, IFN-γ |
cydA | Fw: GGCGTTTGCATCCAAGAGTTA Rv: GGTAGTGAAGGCGTTTTTGCTTT | cytochrome d ubiquinol oxidase sub I | Electron transport system | Amirshahi et al., 2011 [22] C. trachomatis. Estradiol and progesterone |
cydB | Fw: TCCACACAACAACGTGTAGG Rv: TAGTAAGACCGAGTCAGCAAAATGG | cytochrome d ubiquinol oxidase sub II | Amirshahi et al., 2011 [22] C. trachomatis. Estradiol and progesterone | |
miaA | Fw: CGCCCACAAGAATAGGGACTT Rv: GACAGCGCATTCCTCATTATCTGA | isopentenylpyrophosphate transferase | Control at the translational level | Amirshahi et al., 2011 [22] C. trachomatis. Estradiol and progesterone |