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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.
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BMC Genomics

ISSN: 1471-2164

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