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Table 1 Zinc dependent differentially expressed genes

From: Identification of a lineage specific zinc responsive genomic island in Mycobacterium avium ssp. paratuberculosis

   Orthologue genes (% similarity)     
RCNa Locus tag Mtb MAA q-valueb Fold changec Putative functiond COGe
- MAP4069c - MAV_4568 (99.3) <0.0001 9.5 unknown function S
- MAP4065 Rv0924c (43.62) MAV_4571 (99.8) 0.0044 3.16 putative cation-transport membrane protein, NRAMP family P
- MAP3788 Rv0292 (61.6) MAV_4860 (98.3) <0.0001 25.48 ESX type VII secretion protein EccE -
- MAP3787 Rv0291 (69.9) MAV_4862 (98.9) <0.0001 30.43 type VII secretion-associated serine protease MycP3 -
- MAP3786 Rv0290 (80.1) MAV_4863 (99.4) <0.0001 15.38 type VII secretion integral membrane protein EccD -
- MAP3785 Rv0289 (77.0) MAV_4864 (99.7) <0.0001 22.69 putative ESX-3 secretion-associated protein -
- MAP3784 Rv0288 (79.0) MAV_4865 (100) <0.0001 22.09 Esat-6 like protein EsxH S
- MAP3783 Rv0287 (84.5) MAV_4866 (100) <0.0001 20.81 Esat-6 like protein EsxG -
- MAP3782 Rv0286 (41.85) MAV_4867 (98.6) <0.0001 22.37 PPE-family protein N
- MAP3781 Rv0285 (85.1) MAV_4868 (99.0) <0.0001 29.76 PE-family protein -
- MAP3780 Rv0284 (84.9) MAV_4869 (93.47) <0.0001 23.91 type VII secretion protein EccCa/type VII secretion protein EccCb D
- MAP3779 Rv0283 (72.6) MAV_4870 (87.5) <0.0001 37.19 hypothetical protein, ESX type VII secretion protein EccB, -
- *MAP3778 Rv0282 (86.5) MAV_4871 (91.5) <0.0001 28.87 putative ESX-3 type VII secretion system protein EccA O
- MAP3776c Rv2059 (51.45) MAV_0583 (46.3) <0.0001 13.81 hypothetical protein, putative permease P
- MAP3775c Rv2397c (52.38) MAV_0582 (55.5) <0.0001 15.26 ATPase component of Mn/Zn ABC-type transporter P
- MAP3774c Rv2060 (37.0) MAV_0581 (51.89) <0.0001 17.58 ABC-type Mn2+/Zn2+ transport system, permease component P
- MAP3773c Rv2359 (56.8) MAV_2036 (58.06) <0.0001 16.92 Fe2+/Zn2+ uptake regulation protein, Fur family protein P
- *MAP3772c - - <0.0001 140.73 cobW-like cobalamin synthesis, metal chaperone R
rpmE2 MAP3771 - - <0.0001 183.4 50S ribosomal protein L31 J
- *MAP3770 Rv0106 (66.1) MAV_4874 (73.5) <0.0001 218.07 cobW-like cobalamin synthesis, metal chaperone R
rpmG *MAP3769c Rv2057c (85.2) MAV_4876 (93.5) <0.0001 191.92 50s ribosomal protein L33 J
rpsN2 MAP3768c Rv2056c (81.2) - <0.0001 194.0 30S ribosomal protein S14 RpsN2 J
rpsR2 MAP3767c Rv2055c (77.2) MAV_0076 (84.61) 1.0 22.32# 30S ribosomal protein S18 J
- MAP3766 - MAV_4878 (85.1) <0.0001 6.83 hypothetical protein, putative permease R
- *MAP3765 Rv3738c (80.43) MAV_4879 (76.1) <0.0001 24.43 PPE-family protein N
pks2 *MAP3764c Rv1180 (78.67) MAV_2370 (68.0) <0.0001 23.31 polyketide synthase Pks2 Q
papA3_2 MAP3763c Rv1182 (68.24) MAV_2723 (66.35) <0.0001 21.0 polyketide synthase associated protein papA3 -
- MAP3762c Rv1524 (67.83) MAV_3994 (70.74) <0.0001 35.58 putative glycosyl hydrolase GC
- MAP3761c Rv1517 (50.86) MAV_1758 (50.58) <0.0001 5.03 unknown function -
- MAP3760c Rv2952 (72.0) MAV_3877 (50.58) <0.0001 4.02 unknown function H
fadD28 MAP3752 Rv3826 (61.4) MAV_2374 (67.1) <0.0001 3.4 acyl-CoA synthetase IQ
mmpL4_5 MAP3751 Rv0507 (64.9) MAV_3863 (65.4) <0.0001 26.35 MmpL-family protein, MmpL4_5 R
mmpS1 MAP3750 Rv0451c (69.49) MAV_3864 (68.37) <0.0001 67.0 putative membrane protein -
- MAP3749 Rv2750 (49.46) MAV_2946 (60.0) <0.0001 163.04 3-ketoacyl-ACP reductase, caRveol dehydrogenase IQR
IS1110 MAP3748c Rv2177c (50.0) MAV_1059 (43.31) 0.00012 4.42 IS1110 transposase L
cobW *MAP3747c Rv0106 (59.53) MAV_4874 (58.39) <0.0001 41.47 putative cobalamin synthesis protein R
sidB MAP3741 Rv2383c (45.86) MAV_2009 (66.47) 0.0 150.4# putative thioester reductase -
sidA *MAP3740 Rv2383c (45.86) MAV_2013 (47.41) <0.0001 237.0 putative non-ribosomal peptide synthase, thioester reductase Q
sidG *MAP3739c Rv2333c (44.2) - <0.0001 270.0 MFS transporter permease G
- MAP3738c - - <0.0001 121.73 type12 methyltransferase R
- *MAP3737 Rv0280 (63.9) MAV_4872 (59.37) <0.0001 75.65# PPE-family protein N
mptA *MAP3736c Rv1348 (50.0) MAV_1566 (51.37) <0.0001 39.4 hypothetical protein, ABC-transporter ATPase V
mptB MAP3735c Rv1348 (54.48) MAV_1566 (54.16) <0.0001 78.18 ABC transporter ATP-binding protein V
mptC MAP3734c Rv1348 (59.33) MAV_1566 (58.36) <0.0001 19.0 putative ABC transporter ATPase and permease component V
mptD MAP3733c - - <0.0001 5.77 unknown function -
mptE MAP3732c - - <0.0001 13.14 ABC-type cobalt transport system, permease component P
mptF MAP3731c Rv3663c (44.93) - <0.0001 4.11 ABC-type cobalt transport system, ATP binding component P
- MAP3632 Rv0190 (89.6) MAV_4988 (100) <0.0001 5.23 unknown function S
- MAP3626c - MAV_4993 (100) <0.0001 29.25 metallothionein -
- MAP3492 Rv3401 (86.0) MAV_4352 (99.7) <0.0001 10.27 putative glycosyl hydrolase G
- MAP3491 Rv3400 (77.3) MAV_4350 (98.9) <0.0001 22.04 hypothetical protein, beta-phosphoglucomutase hydrolase R
- MAP3047 Rv3013 (88.0) MAV_3861 (100) <0.0001 16.0 ACT domain-containing protein TK
- MAP2999 Rv2963 (80.7) MAV_3787 (99.2) <0.0001 16.82 hypothetical protein R
- MAP2414c Rv1348 (79.6) MAV_1566 (97.7) <0.0001 5.0 iron ABC transporter permease V
- MAP2412c - MAV_1568 (98.6) <0.0001 6.0 phosphotransferase enzyme family protein R
trpE2 MAP2205c Rv2386c (74.0) MAV_1792 (99.6) <0.0001 4.54 salicylate synthase MbtI EH
mbtB MAP2177c Rv2383c (72.1) MAV_2009 (98.6) <0.0001 10.0 Phenyloxazoline synthase Q
- MAP2176c Rv2383c (58.02) MAV_2010 (98.6) <0.0001 10.0 phenyloxazoline synthase, thioesterase Q
mbtC MAP2175c Rv2382c (71.9) MAV_2011 (99.1) <0.0001 5.75 polyketide synthase, erythronolide synthase Q
mbtD MAP2174c Rv2381c (53.08) MAV_2012 (98.2) <0.0001 4.43 MbtD, polyketide synthase Q
mbtE MAP2173c Rv2380c (74.38) MAV_2013 (96.8) <0.0001 4.35 MbtE, partial linear gramicidin synthetase subunit D Q
- MAP2172c Rv2380c (51.11) MAV_2013 (99.3) <0.0001 5.58 fmnh2-utilizing oxygenase Q
smtB MAP2138 Rv2358 (74.4) MAV_2037 (99.3) 0.00034 - 7.5 ArsR family transcriptional regulator K
- MAP1977c Rv0560c (43.04) MAV_2216 (98.6) <0.0001 12.5 CheR methyltransferase, SAM binding domain R
- MAP1555c Rv1344 (77.8) MAV_2873 (100.0) <0.0001 7.81 acyl carrier protein IQ
fadD33_2 MAP1554c Rv1345 (70.0) MAV_2874 (99.2) <0.0001 3.67 acyl-CoA synthetase IQ
fadE14 MAP1553c Rv1346 (81.9) MAV_2876 (99.2) <0.0001 3.99 acyl-CoA dehydrogenase FadE14 I
- *MAP0489c Rv2059 (63.1) MAV_0583 (99.0) <0.0001 27.14 putative Zinc ABC transporter, periplasmic-binding protein ZnuA P
- MAP0488c - MAV_0582 (99.3) <0.0001 30.0 putative Zinc ABC transporter, ATP-binding protein ZnuC P
- MAP0487c Rv2060 (84.2) MAV_0581 (99.7) <0.0001 10.07 putative Zinc ABC transporter, transmembrane protein ZnuB P
  1. aReference Common Name.
  2. bq-value of differentially expressed genes MAPwt standard culture vs. MAPwt TPEN culture calculated by Rockhopper analysis. A q-value < 0.01 is considered as significant.
  3. cgene expression values of MAPwt TPEN culture divided by gene expression values of MAPwt standard culture from RNA-sequencing.
  4. dPutative function based on Blast2Go or NCBI blastx analysis.
  5. eFunctional classification of proteins has been performed by use of COG database with MAP-K10 as a reference (http://www.ncbi.nlm.nih.gov/sutils/coxik.cgi?gi=380). (C) Energy production and conversion, (D) Cell cycle control, (E) Amino acid transport and metabolism, (G) Carbohydrate transport and metabolism, (H) Coenzyme transport and metabolism, (I) Lipid transport and metabolism, (J) Translation, (K) Transcription, (L) Replication, recombination and repair, (N) Cell motility, (O) Posttranslational modification, protein turnover, chaperones, (P) Inorganic ion transport and metabolism, (Q) Secondary metabolites biosynthesis, transport and catabolism, (R) General function prediction only, (S) Function unknown, (T) Signal transduction mechanisms, (V) Defense mechanisms.
  6. *genes preceded by predicted FurB binding sites from FIMO analysis.
  7. #zinc dependent expression was confirmed by qRT-PCR.