Results

M. smegmatisΔupk Sequence comparison of Upk homologues

Protein sequences of E. coli undecaprenyl-phosphokinase (BacA), M. smegmatis undecaprenyl-phosphokinase (Upk), and M. tuberculosis Upk were compared by clustAl analysis (Fig. 6A). Both mycobacterial proteins showed 38 % identity to E. coli BacA and about 50 % similarity. ClustAl comparison of M. smegmatis and M. tuberculosis Upk revealed 73 % identity and 78 % similarity (Fig 6B). Highly conserved features were visible for all three homologues

Fig. 6 Protein sequence comparison with clustAl alignment reveals highly conserved features of E. coli BacA and mycobacterial Upk. Identity of E. coli to M. smegmatis and M. tuberculosis is 38 % and similarity 50 %(A). Identity of M. smegmatis to M. tuberculosis is 73 %, and similarity 78 %(B). Color definitions: blue - all amino acids of a column are identical; red - more than half of the amino acids of a column are identical or belong to one of the strong groups (amino acids with strong similarities); orange - more than half of the amino acids of a column belong to one of the weak groups (amino acids with weak similarities), or amino acids that could be grouped into a weak group with every amino acid of the same column belonging to a strong group that is marked red.

Construction of Δ upk mutant of M. smegmatis mc2 155

An in-frame, unmarked deletion of the M. smegmatis upk gene was created by a two-step-method [58]. Regions of 879 bp and 945 bp flanking the upk gene in M. smegmatis were amplified by PCR and inserted into pYUB657. Thus 96% of the wildtype upk gene was deleted. The mutated copy of upk was introduced into M. smegmatis by electroporation. Hyg^R transformants which displayed a Suc^S phenotype were assayed for recombination by Southern blot. There is the possibility of integration upstream or downstream of the target gene by single crossover. A mutant in which the template plasmid has inserted upstream, resulting in 11,547 bp and 7,337 bp fragments on Southern blot (Fig 7., southern blot a) was chosen for further analysis. A culture of this single crossover strain was grown overnight in complete medium without hygromycin. This period of growth allowed double crossover events to occur, followed by plasmid loss. Deletion or preservation of the wildtype allele occur with equal probability. Two out of 6 analyzed clones displayed the characteristics of a upk deletion mutant (Fig. 7, southern blot b). The mutant strain was named M. smegmatisΔupk. A complementation strain was constructed, using pMV262-rv2136c, a multicopy plasmid expressing the M. tuberculosis H37Rv homologue of the upk gene under control of the M. bovis BCG groEL2 (Hsp60) promoter. The parent plasmid, pMV262, is an episomal E. coli -mycobacteria shuttle plasmid.

Fig. 7 An in-frame, unmarked deletion of upk was generated in M. smegmatis by a two step approach. In the first step, the counterselectable suicide plasmid pYUB657 carrying the deletion allele of upk recombined with the bacterial chromosome. Southern blot analysis confirmed the recombination event. Two orientations are possible (southern blot a: lane 1 and 2). Clone 2 was selected. In the second step the plasmid loops out in the absence of hygromycin selective pressure. The deletion allele or the wildtype copy of upk are lost with equal probability. Deletion of upk was verified by Southern blot (Southern blot b). Lane 1 and 5 are deletions, the others are wildtype. For the following studies clone number 1 was selected.
Differential abundance of peptidoglycan and colony morphology

Bacteria were grown on 7H10 agar plates. While wildtype M. smegmatis showed dome-like morphology, Δupk mutant colonies exhibited caved-in structures (Fig. 8). Although this observation suggests that the cell wall is affected, examination by electron microscopy revealed no differences (Fig. 8). Yet, specific immunogold-staining of peptidoglycan revealed a lower number of gold-particles associated with the cell surface of the Δupk mutant (Table 1). Twenty electron microscopy images of stainings of wildtype and the Δupk mutant were examined. For wildtype, 241 particles were counted of which 27% were surface associated. Of the 225 particles counted on the Δupk mutant bacteria, only 13% were surface associated (Fig. 9).

Fig. 8 Differential colony morphology of M. smegmatis mc²155 and M. smegmatis mc²155Δupk. Mutant colonies have caved-in structures lacking dense cores (1a: wildtype and 2a: Δupk mutant). Using electron microscopy, there is no visible difference in cell wall architecture (1: wildtype and 2: Δupk mutant).

Fig. 9 Distribution of gold particles in an anti-peptidoglycan immuno-gold stain. Twenty electron microscopy images of wildtype and the Δupk mutant were examined. For wildtype, 241 particles were counted of which 27% were surface associated. Of the 225 particles counted on the Δupk mutant bacteria, 13% were surface associated.

gold particles total

particles in the cytoplasm

particles on the surface

Wildtype

241

176

73%

65

27%

Δupk

225

195

86,7%

30

13,3%

Table 1: distribution of gold particles in anti peptidoglycan immuno-gold stain.

Sensitivity to bacitracin

As described above, Δupk mutants are expected to be more sensitive to bacitracin than wildtype M. smegmatis. This issue was investigated by the alamar blue assay. Alamar blue is a redox-dye that converts from blue to red upon reduction, reflecting a measure of growth [59]. Bacteria were incubated over night in 7H9 complete medium supplemented with serial dilutions of bacitracin (0 U/ml – 2,500 U/ml). Next day, alamar blue was added and fluorescence at 570 nm was measured. The M. smegmatisΔupk mutant showed no growth at a concentration of 500 U/ml bacitracin, whereas wildtype reached 55% of its maximal growth (Fig. 10). The reconstituted strain M. smegmatisΔupk + pMV262-rv2136c failed to regain wildtype growth but displayed an intermediate phenotype.

Fig. 10 Sensitivity assay to bacitracin. M. smegmatis mc²155 (■), M. smegmatis mc²155Δupk (□),and M. smegmatis mc²155Δupk + pMV262-rv2136c (●) were incubated with different concentrations of bacitracin over night. Next day alamar blue was added and growth was measured at 570 nm. The Figure shows 1 representative experiment of 3 with similar results.

* Curves were significantly different at 500 and 1000 U bacitracin / ml according to Mann Whitney test (P<0.0001).
Accelerated clearance from infected macrophages

We wanted to find out whether upk homologues contribute to virulence of pathogenic mycobacteria. Therefore we chose the model of macrophage infection. Although, M. smegmatis fails to persist in macrophages it was possible to compare the survival times of M. smegmatis and the Δupk mutant in murine bone marrow derived macrophages. After infection, bacteria were cleared quickly. The time needed to kill half of the bacterial number upon infection differed between M. smegmatis wildtype (98 min), M. smegmatisΔupk mutant (27 min) and the reconstituted mutant strain (126 min) (Fig. 11).

Fig. 11 Infection of murine bone marrow derived macrophages. M. smegmatis mc²155 (■), M. smegmatis mc²155Δupk (□) and M. smegmatis mc²155Δupk + pMV262-rv2136c (●) were used at a MOI of 200. After 27 min half of M. smegmatisΔupk mutants were killed. This was true for wildtype M. smegmatis after 98 min and after 126 min for Δupk mutant carrying pMV262-rv2136c. The Figure shows 1 representative experiment of 2 with similar results.
Growth properties and biofilm formation

Bacterial growth curves exhibited slightly slower growth of the M. smegmatisΔupk mutant compared to M. smegmatis wildtype after 9 h in 7H9 complete medium (Fig. 12A) and after 9 and 24 h in biofilm medium (Fig. 12B). Nevertheless, after 24 h, in 7H9 complete medium and after 72 h in biofilm medium, growth characteristics of all M. smegmatis strains adapted.

Fig. 12 Growth curves. M. smegmatis mc²155 (■), M. smegmatis mc²155Δupk (□), and M. smegmatis mc²155Δupk + pMV262-rv2136c (●) grown at 37°C in 7H9 complete medium (A) and biofilm medium (B). The Figure shows 1 representative experiment of 2 with similar results.

According to Mann Whitney test, growth curves in 7H9 complete medium (A) were not different whereas growth of M. smegmatis wildtype was significantly different at 9 and 24 h in biofilm medium(B) compared to the M. smegmatisΔupk strain and the reconstituted strain (P<0.0001).

M. smegmatis forms biofilms under natural conditions [60]. We determined whether deletion of the upk gene affected biofilm formation in vitro and in vivo. After 4 to 5 days shaking at RT in biofilm medium, biofilms were analyzed. Wildtype bacteria completely covered the surface whereas Δupk M. smegmatis only produced scattered islands of biofilm (Fig. 13).

Fig. 13 Differential biofilm formation. M. smegmatis mc²155 (A, C) and M. smegmatis mc²155Δupk (B, D) were grown for 4 to 5 days at room temperature in biofilm medium and stained with crystal violet. The mutant exhibited impaired biofilm development. Rhodamine auramine staining (C, D) visualized even structures (highlighted by white arrows) only in wildtype biofilms.

Principally, an intact biofilm is characterized by a matrix consisting of extracellular polymer substances (EPS). Such a matrix was clearly visible for wildtype M. smegmatis, whereas the Δupk mutant grew in separated single cells (Fig. 13). Additional studies to follow in vivo biofilm development were performed. M. smegmatis wildtype applied to a mouse penis induced smegma in 65 % of the animals, whereas smegma development upon application of Δupk deletion mutant was observed for 42% only, which was about background level (Fig. 14A). Groups consisted of 10 animals each.

Fig. 14A In vivo biofilm formation. Penises of C57BL/6 mice were exposed to medium, wildtype M. smegmatis, and Δupk deletion mutant. The Figure shows combined results of 2 independent experiments with similar results. Before application of the M. smegmatis strains, mice had a clean penis (14B). A penis with an over night grown smegma is depicted in 14C. 14D shows a smegma plug removed from a penis.
Summary M. smegmatis mc2155 Δ upk
The M. smegmatis upk gene was identified and an in-frame, unmarked deletion mutant was generated. The absence of Upk influenced bacitracin sensitivity, peptidoglycan synthesis, survival in macrophages, growth properties, and biofilm formation in vitro and in vivo. In vitro biofilms of M. smegmatis Δupk mutant were characterized as scattered islands of bacteria compared to a completely covered surface observed for wildtype bacteria. The M. smegmatis Δupk strain is the first to express a phenotype in a newly developed in vivo mouse model of biofilms.

M. tuberculosisΔupk (and construction of Mycobacterium bovis BCG Δupk) Construction of Δ upk mutant strains of M. tuberculosis and M. bovis BCG

A temperature sensitive (ts) TM4 phage delivery system was used to generate hygromycin-marked knockout mutants in M. tuberculosis and M. bovis BCG. Flanking regions to the M. tuberculosis upk gene were cloned next to a hygromycin resistance cassette and fused to the phage genome. Recombinant ts phages were amplified at 30°C using M. smegmatis growing in top agars as a host. At 37°C, phages were impaired to become lytic and could be used to transduce M. tuberculosis H37Rv and M. bovis BCG. The recombinant phages transferred their DNA into the bacteria. Flanking regions induced double crossover events, thus exchanging the upk gene with a hygromycin resistance cassette, which subsequently was verified by Southern blot (Fig. 15). The mutant strains were named: M. tuberculosisΔupk and M. bovis BCG Δupk.

Fig. 15 Construction of upk knockout mutants in M. tuberculosis and M. bovis BCG. Knockout phage genome phAE159-Δupk was generated by ligation of the plasmid pKO-upk and the phage genome phAE159 TM4 (A). Four phages were tested for temperature-sensitivity and revealed the expected phenotype- lysis at 30°C but not at 37°C (B). # 4 was picked, amplified and used for transduction of M. tuberculosis and M. bovis BCG. Lane 4 and 6 represent upk deletion mutants for M. tuberculosis H37Rv and M. bovis BCG, verified by Southern blot analysis (C).

A complementation strain of M. tuberculosis was constructed using pMV262-rv2136c, a multicopy plasmid expressing upk under control of the groEL2 (Hsp60) promoter of M. bovis. The parent plasmid, pMV262, is an episomal E. coli -mycobacteria shuttle-plasmid. M. tuberculosis was difficult to transform by electroporation. In many cases, only the antibiotic resistance was transformed and other parts of the plasmid were lost. Thus, the appropriate size of the resistance cassette and the rv2136c gene (data not shown) was verified by PCR for kanamycin resistant colonies of M. tuberculosis H37Rv Δupk mutants, transformed with pMV262-rv2136c. Additionally, whole DNA was prepared from a positive clone and used for transformation of E. coli DH5α. Subsequently, the plasmid was purified and compared to the original vector. BamHI digest, released the rv2136c insert. SalI digest was used to verify the correct orientation of the insert. The fragments were analyzed by gelelectrophoresis and appeared as the same size as the original vector. The recombinant M. tuberculosisΔupk knockout clone carrying this vector was used as the complementation strain (Fig. 16). Transcription levels of upk were determined by RT-PCR in relation to rv2946c, a gene transcribed at the same level inthe M. tuberculosis H37Rv Δupk mutant and wildtype. Transcription of the upk gene under control of the groEL 2 promoter was 3.51 fold higher than rv2946c-transcription and 201.56 fold lower than transcription of upk in the wildtype strain under control of the natural promoter in late logarithmic growth phase.

Fig. 16 Comparison of the original reconstitution vector pMV262-rv2136c, and the reconstitution vector purified from an electroporated Δupk strain. Lanes # 1 and # 2 show the pattern of the original insert with accurate orientation. Lanes # 3 and # 4 confirm this pattern for the vector purified from the reconstitution strain.
Growth curve

Growth properties in 7H9 medium were examined for the 3 strains: wildtype, Δupk mutant, and reconstitution. OD₆₀₀ was measured once a day. The M. tuberculosisΔupk mutant showed no differences in growth rate compared to wildtype whereas the complementation strain grew more slowly (Fig. 17).

Fig. 17 Growth curves. M. tuberculosis H37Rv (■), M. tuberculosis H37Rv Δupk (□), and M. tuberculosis H37Rv Δupk + pMV262-rv2136c (∙) were grown at 37°C in 7H9 complete medium. The Figure shows 1 representative experiment of 2 with similar results.
In vitro assays

Colonies of M. tuberculosis wildtype, the M. tuberculosisΔupk mutant and the reconstituted strain were of the same shape (data not shown). The attenuated strain M. tuberculosis H37Ra is known to behave differently compared to M. tuberculosis H37Rv in the following in vitro assays: Neutral red staining, cording assay, and pellicle culture. The H37Ra-strain is not stainable with neutral-red [61] (Fig. 18A).
For virulent M. tuberculosis H37Rv, bacterial cord-factors e.g. trehalose dimycolate (TDM; [62] are necessary for growth in cords on a surface in non-shaking cultures [63].
After 2 to 3 weeks, cultures of M. tuberculosis grown without shaking in Sauton medium, form pellicles on top of the medium and bacteria push each other up the wall of the tube.

All M. tuberculosis strains were examined in these 3 assays:

The strains were treated with neutral red. Pellets of stained Δupk knockout mutant and complementation strain exhibited red color like H37Rv wildtype did, thus revealing no phenotype-differences (Fig. 18A).

Also cording was not affected by loss of upk. All strains were stained with rhodamine auramine (Fig. 18B).

The M. tuberculosis strains revealed phenotype-differences in case of pellicle formation. The Δupk mutant was hampered in pellicle formation and the complementation strain developed a gapless, smooth pellicle in contrast to the rough pellicle of M. tuberculosis wildtype (Fig. 18C).

Fig. 18 Assays on M. tuberculosis behavior under defined conditions. Neutral-red stained M. tuberculosis H37Rv, M. tuberculosisΔupk, and the reconstitution strain but not M. tuberculosis H37Ra (A). Wildtype, mutant, and reconstitution strain grew in cords (B). M. tuberculosis wildtype formed a heterogeneous pellicle whereas M. tuberculosisΔupk was retarded in pellicle formation, and the reconstituted mutant exhibited a smooth pellicle (C)
Proteome and transcriptome analysis

Cultures of M. tuberculosis H37Rv and the Δupk mutant were grown to late log-phase (OD₆₀₀ = 1.0) and whole cell lysates, as well as RNA were purified.

Proteome analysis was performed with 3 independent protein lysates of both strains, M. tuberculosis wildtype and M. tuberculosisΔupk mutant. Each sample was analyzed on 2 gels. The comparative proteome analysis of 12 gels (6 wildtype and 6 mutant) revealed 45 spots of differential relative intensity. For the Δupk mutant, 23 spots belonged to the group of higher intensity and 22 spots exhibited lower intensity (Table 2) compared to M. tuberculosis wildtype. Representative examples are depicted in Figure 19. The 2-DE gels were first evaluated visually. Subsequently, the gels were re-evaluated by means of the image analysis program PDQuest. This software allowed verification of significance of the results by t-test and offered the possibility to quantify spot intensities.

In parallel to determine and compare gene expression profiles, RNA of M. tuberculosis H37Rv and the Δupk strain were purified and hybridized to a M. tuberculosis array. Wildtype and mutant showed a high number of differentially regulated genes. The 20 most significantly regulated genes of 2 independent experiments are summarized in Figures 20 and 21.

Correlation of the results of proteome and transcriptome was limited. Comparing M. tuberculosisΔupk and M. tuberculosis wildtype, proteins of higher spot intensity, such as Rv0341 and Rv2462 had a higher transcription rate, too. And proteins of lower spot intensity, like Rv1912 and Rv0125 also had a lower transcription rate. However, Rv2031c / HspX was a protein of high abundance in M. tuberculosisΔupk whole cell lysates, compared to M. tuberculosis wildtype, but gene expression did not differ between both strains. HspX is of interest, because it is one of several proteins produced during persistence of bacteria under low oxygen conditions and within granulomas, but at a lower level during logarithmic growth phase [64,65]. The examined bacterial cultures were harvested at late logarithmic growth phase (OD₆₀₀ = 0.8 - 1).

* Spot numbers are according to discovery order of spots of different intensity. “⇑” means higher spot intensity.
**see Table 4: tuberculist classification of functional categories
Spot number*

Identity

Functional category **

Fold change
(mutant strain compared to wildtype)

⇑ 08

NADH dehydrogenase chain E
(nuoE, Rv3149 )

7

new spot

⇑ 09

Antigen 84
(wag31, Rv2145c )

3

new spot

⇑ 11

Hypothetical protein Rv0341 and
glu-tRNA-gln amidotransferase, subunit B (gatA, Rv3011c )

3, 2

new spot

⇑ 17

not identified

new spot

⇑ 18

not identified

new spot

⇑ 19

not identified

new spot

⇑ 20

not identified

new spot

⇑ 01

14 kDa antigen
(hspX, Rv2031c )

0

12.0

⇑ 03

14 kDa antigen
(hspX, Rv2031c )

0

8.0

⇑ 03b

14 kDa antigen
(hspX, Rv2031c )

0

6.1

⇑ 12

[beta]-ketoacyl-ACP synthase

(kasB, Rv2246 )

1

3.7

Spot number*

Identity

Functional category **

Fold change
(mutant strain compared to wildtype)

⇑ 03a

14 kDa antigen
(hspX, Rv2031c )

0

3.3

⇑ 05

Hypothetical protein Rv1284

10

3.0

⇑ 17

not identified

2.6

⇑ 04

not identified

2.3

⇑ 12a

2.3

⇑ 04

not identified

2.3

⇑ 14

not identified

2.2

new ⇑ 01

Putative transcriptional regulator
( Rv1956 )

9

2.2

new ⇑ 05

Two-component response regulator
(NarL, Rv0844c )

9

2.1

⇑ 13

Chaperone protein, similar to trigger factor
(tig, Rv2462c )

3

2.0

⇑ 07 left

Hypothetical protein Rv0207c

10

2.0

⇑ 07 right

Hypothetical protein Rv0207c

10

2.0

Table 2a: M. tuberculosis H37Rv Δ upk protein spots of higher relative intensity

* Spot numbers are according to discovery order of spots of different intensity. “⇓” means lower spot intensity.
**see Table 4: tuberculist classification of functional categories
Spot number*

Identity

Functional category **

Fold change
(mutant strain compared to wildtype)

⇓ 06

Hypothetical protein Rv0481c

16

lost spot

⇓ 07

Hypothetical protein Rv0968

10

lost spot

⇓ 08

Hypothetical protein Rv0968

10

lost spot

⇓ 12

not identified

lost spot

⇓ 18

3-hydroxyacyl-CoA dehydrogenase
(fadB5, Rv1912c )

1

lost spot

⇓ 04

not identified

10.3

⇓ 11

Hypothetical protein Rv2302

10

7.4

⇓ 24

Probable serine protease
(pepA, Rv0125 )

7

5.0

⇓ 02

Hypothetical protein Rv3615c

10

4.9

⇓ 03

Hypothetical protein Rv3615c

10

4.6

⇓ 09

Hypothetical protein Rv0967

10

3.7

⇓ 21

not identified

3.1

⇓ 13

possible Soj/para-related protein
Rv3213c

3

2.9

⇓ 01

not identified

2.8

⇓ 23

Hypothetical protein Rv3651

10

2.8

⇓ 7a

Hypothetical protein Rv0968

10

2.4

Spot number*

Identity

Functional category **

Fold change
(mutant strain compared to wildtype)

⇓ 05

Hypothetical protein Rv3369

10

2.1

⇓ 16

Possible haloalkane dehalogenase Rv1833c

7

2.1

⇓ 10

Hypothetical protein Rv1558

10

2.1

⇓ 22

Ribose-phosphate pyrophosphokinase
(prsA, Rv1017c )

7

2.1

⇓ 06a

Hypothetical protein Rv0481c

16

2.0

⇓ 14

Possible ketoacyl reductase Rv1544

1

2.0

Table 2b: M. tuberculosis H37Rv Δ upk protein spots of lower relative intensity

Fig. 19 Examples of protein spots with differential relative intensity in 2-DE patterns of whole cell lysate proteins of the upk mutant strain (B, D, F) and the M. tuberculosis H37Rv control (A, C, E). The same protein can give rise to multiple spots as in the case of Rv2031c/HspX (picture E).

*see Table 4: tuberculist classification of functional categories
rv-number

Synonyms

Description

Functional category *

rv2243

mtFabD

malonyl CoA-Acyl carrier protein

transacylase FabD (malonyl CoA:AcpM acyltransferase)

1

rv0873

fadE10

probable acyl-CoA dehydrogenase FadE10

1

rv3136

PPE

PPE family protein

6

rv3407

conserved hypothetical protein

10

rv2247

accD6

acetyl/propionyl-CoA carboxylase (beta subunit) AccD6

1

rv1871

conserved hypothetical protein

10

rv0702

rplD

probable 50s ribosomal protein L4 RplD

2

rv1103c

conserved hypothetical protein

10

rv2879c

conserved hypothetical protein

10

rv0874c

conserved hypothetical protein

10

rv3801c

fadD32

probable fatty-acid-CoA ligase FadD32 (fatty-acid-CoA synthetase) (fatty-acid-CoA synthase)

1

rv2245

kasA

3-oxoacyl-[acyl-carrier-protein] synthase 1 KasA (beta-ketoacyl-ACP synthase) (KAS I)

1

rv1094

desA1

probable acyl-[ acyl-carrier-protein] desaturase DesA1 (acyl-[ACP] desaturase) (stearoyl-ACP desaturase) (protein Des)

1

rv1736c

narX

probable nitrate reductase NarX

7

rv0685

tuf

probable iron-regulated elongation factor Tu Tuf (Ef-Tu)

2

rv0313

conserved hypothetical protein

10

rv-number

Synonyms

Description

Functional category *

rv3548c

probable short-chain type dehydrogenase / reductase

7

rv3583c

possible transcription factor

9

rv1174c

TB8.4

low molecular weight T-cell antigen TB8.4

3

rv1821

secA2

possible preprotein translocase ATPase SecA2

3

Table 3a: M. tuberculosis H37Rv Δ upk genes of higher transcription rate compared to wildtype

*see Table 4: tuberculist classification of functional categories
rv-number

Synonyms

Description

Functional category *

rv2909c

probable 30s ribosomal protein s16 Rpsp

2

rv2649

probable transposase for insertion sequence element Is6110

5

rv2648

probable transposase for insertion sequence element Is6110

5

rv2278

probable transposase

5

rv1669

hypothetical protein

16

rv1276c

conserved hypothetical protein

10

rv3281

conserved hypothetical protein

10

rv1663

pks17

Probable polyketide synthase Pks17

1

rv2168c

probable transposase

5

rv1066

conserved hypothetical protein

10

rv3280

accD5

probable propionyl-CoA carboxylase beta chain 5 AccD5 (Pccase) (propanoyl-CoA:carbon dioxide ligase) key enzyme in the catabolic pathway of odd-chain-fatty acids

1

rv2666

probable transposase for insertion sequence element IS1081 (fragment)

5

rv0894

possible transcriptional regulatory protein (possibly LuxR-family)

9

rv1275

lprC

possible lipoprotein LprC

3

rv3824c

papA1

probable conserved polyketide synthase associated protein PapA1, thought to be involved in lipid metabolism

1

rv2717c

conserved hypothetical protein

10

rv-number

Synonyms

Description

Functional category *

rv2013

possible transposase

5

rv1047

probable transposase

5

rv2011

conserved hypothetical protein

10

rv2528c

mrr

probable restriction system protein Mrr

2

Table 3b: M. tuberculosis H37Rv Δ upk genes of lower transcription rate compared to wildtype

Tuberculist classification of functional categories

# 0

virulence, detoxification, adaptation

# 1

lipid metabolism

# 2

information pathways

# 3

cell wall and cell processes

# 4

stable RNAs

# 5

insertion seqs and phages

# 6

PE/PPE

# 7

intermediary metabolism and respiration

# 8

unknown

# 9

regulatory proteins

# 10

conserved hypotheticals

# 16

conserved hypotheticals with an orthologue in M. bovis

Table 4: functional categories

Thirty percent of the genes with a higher transcription rate in M. tuberculosisΔupk mutant compared to M. tuberculosis wildtype encode for proteins involved in lipid metabolism, additional 10 % were cell wall and cell-process related genes. Taken together, 40 % of the most significantly up-regulated genes were involved in the cell envelope complex. This corresponds to the observation that within the group of higher intensity protein spots, 37 % belong to the cell envelope complex.

Twenty percent of the genes with a lower transcription rate in M. tuberculosisΔupk encode for proteins which are related to the cell envelope complex. Again, this corresponds to 21 % of the protein spots with lower intensity which are related to cell envelope complex.

Fig. 20 Percentage distribution of gene expression profiles and differential protein spot intensities according totuberculist classification of functional categories. Lipid metabolism was the most prominent fraction within the group of up-regulated genes for the Δupk mutant (A) and insertion sequences and phages protrude as a cluster of genes to be turned off (B).

Global analysis pointed to especially one significantly upregulated gene cluster of transcriptome analysis: fabD (rv2243), kasA (rv2245), and accD6 (rv2247), and additionally from proteome analysis: KasB (Rv2246). This represents 4 members of a 5 gene operon (Fig. 21), consisting of FAS-II system encoding enzymes involved in biosynthetic pathway for long-chain fatty acids and precursors of mycolic acids which are part of MAPc. The higher transcription rate of a FAS-II system related operon in the case of the Δupk deletion mutant may reflect a mechanism to overcome the upk deficiency. The rv2244 gene and its geneproduct were inconspicuous concerning transcriptome and proteome analysis.

Fig. 21 Genomic organization of the Fas-II system related operon encoding enzymes involved in biosynthetic pathway for long-chain fatty acids. Genes / proteins with higher transcription rate / amount of protein in the upk deletion mutant are highlighted by arrows
Evaluation of sensitivity to antibiotics
The alamar blue assay was used to determine sensitivity to antibiotics in the same way as described for M. smegmatis. Since there was no access to an Elisa-reader under biosafety level 3 (BSL3) conditions, completed assays were documented with a digital camera and visual color change was the value of bacterial growth. Alamar blue turns from blue to red upon reduction, indicating growth. Based on observations with M. smegmatis, the Δupk mutant was expected to be more sensitive to bacitracin. In contrast, no difference between M. tuberculosis H37Rv wildtype and Δupk mutant was detectable. The reconstituted strain was slightly more susceptible to bacitracin at minute concentration differences of the antibiotic. M. tuberculosis H37Rv and M. tuberculosisΔupk were resistant to bacitracin up to a concentration of 20 units / ml (Fig. 20A).

KasA and KasB which are over-expressed in the M. tuberculosisΔupk mutant, had been proposed to contribute to Isoniazid-resistance [66,67]. Sensitivity of the Δupk mutant to this antibiotic was therefore determined. All three examined M. tuberculosis strains were able to grow at concentrations of up to 20 µg Isoniazid / ml (Fig. 22) except for M. tuberculosisΔupk mutant which was slightly more susceptible, rather contradicting profound contribution of KasA to Isoniazid resistance.

Fig. 22 Alamar blue assay. M. tuberculosis H37Rv wildtype (H37Rv), Δupk mutant (Δupk), and the reconstituted mutant (Rec) were tested for sensitivity against bacitracin (A) and Isoniazid (B). Red color indicates growth / resistance, blue indicates no growth / sensitivity. The Figure shows representative experiments of 4 with similar results.
Infection studies
To determine whether the upk deletion influenced growth of the mutant in vivo, C57BL/6 mice were infected intranasally with 1x10³ cfu. Five mice per group, infected with M. tuberculosis H37Rv, M. tuberculosisΔupk, and M. tuberculosisΔupk + pMV262-upk, were sacrificed at day 1 to precisely determine the concentration of the inoculum. At day 30, 60, and 90, bacterial load in lung and spleen were determined (Fig. 23). M. tuberculosis H37Rv showed a characteristic growth curve with a plateau in the lung at 1x10⁷ cfu. In contrast, cfu of the Δupk mutant increased less than a log per lung during the first 30 days and remained at a level of about 1.4 x 10⁴ cfu / lung until day 90. The reconstituted strain reached an almost constant bacterial load of 1.8 x 10³ cfu / lung at day 90. Nevertheless, all 3 strains were able to disseminate and were detected in spleen and liver (data not shown). While the burden of wildtype bacteria in spleen rose up to 1 x 10⁵ cfu / organ by day 60, the burden of the upk mutant did exceed 4.1 x 10³ cfu / spleen at day 30 and decreased afterwards. The phenotype of the reconstituted strain was unexpected and exhibited a slightly lower bacterial load than the M. tuberculosisΔupk strain in lung and spleen.

Fig. 23 Growth of M. tuberculosis wildtype, the upk deficient, and the reconstituted strain in lung and spleen. C57BL/6 mice were infected with 1x10³ cfu. Filled squares represent cfu of wildtype M. tuberculosis, open squares M. tuberculosisΔupk deletion mutant, and filled reconstitution strain. The Figure shows 1 representative experiment of 2 with similar results.

According to Mann Whitney test, bacterial numbers of M. tuberculosis wildtype and M. tuberculosisΔupk mutant were significantly different at day 60 and 90 in lung and spleen (P<0.0001).
Histology
Organs of infected animals, were removed for histological examinations. At day 90 post infection, lungs of M. tuberculosis wildtype and M. tuberculosisΔupk mutant infected mice revealed striking differences. Typically, animals infected with M. tuberculosis H37Rv showed severe pathology in the lung (Fig. 24). Granulomas were formed and a major part of the lung consisted of affected tissue. In the case of upk deficient M. tuberculosis (Fig. 25), granuloma and affected tissue were found but, in contrast to infection with M. tuberculosis wildtype, the majority of the lung appeared unaffected. The same observation was made for the reconstituted strain which failed to mimic the characteristics of the wildtype strain (Fig. 26).

Lung, 90 days post infection with M. tuberculosis H37Rv:

Fig. 24 Lungs of mice infected with M. tuberculosis H37Rv exhibited severe pathology 90 days post infection. Major part of the lung consisted of granulomatous, heavily infiltrated tissue. Only small regions with unaffected alveoli were found.

Lung, 90 days post infection with M. tuberculosis H37Rv Δupk:

Fig. 25 Lungs of mice infected with M. tuberculosis H37Rv Δupk exhibited reduced pathology compared to M. tuberculosis wildtype 90 days post infection. Major part of the lung appeared non-infiltrated. Only small parts with granuloma could be detected.

Lung, 90 days post infection with M. tuberculosis H37Rv Δupk + pMV262-rv2136c:

Fig. 26 Lungs of mice infected with the reconstitution strain of M. tuberculosis H37Rv Δupk exhibited – like M. tuberculosisΔupk - reduced pathology compared to M. tuberculosis wildtype 90 days post infection. Major part of the lung appeared non-infiltrated. Only small parts with granuloma could be detected.
Survival

Knowledge about virulence of a pathogen can be acquired by infection of immunocompromised mice which fail to control disease beyond a certain threshold. Commonly used immunocompromised animal models are i) highly susceptible Rag1^-/- mice which lack T and B cells and hence, fail to mount an adaptive immune response [68] and ii) IFNγ^-/- mice which are deficient in generating the central mediator of protection against tuberculosis. In this study, Rag1^-/- mice were infected with 1x10⁶ cfu mycobacteria. M. tuberculosis wildtype infected mice survived 26 days in the median (range: d23 - d49). Mice infected with M. tuberculosisΔupk survived 70 days in the median (range: d67 - d77) . Survival times of wildtype and mutant infected animals were significantly different according to logrank test (P<0.0001). The reconstituted strain killed mice after day 42 and about 50 % of the mice survived longer than those infected with the Δupk strain (Fig. 27A).

Similar to Rag1^-/- mice, IFNγ^-/- animals were less susceptible to the Δupk mutant strain than to M. tuberculosis H37Rv wildtype. The median survival time of wildtype infected animals was 30 days (range: d26 – d32), and for M. tuberculosis Δupk mutant infected animals, 80 days (range: d63 – d126). Survival times of wildtype and mutant infected animals were significantly different according to logrank test (P<0.0001). Unexpectedly, the reconstituted strain was more attenuated than the mutant (Fig. 27B).

Fig. 27 Survival of immunocompromised mice. Rag1^-/- (A) and IFNγ deficient animals (B) were infected with M. tuberculosis H37Rv(■), upk deficient M. tuberculosis (□), and the reconstituted strain (●), respectively. The experiments were performed with 10 mice per group. Survival of Rag1^-/- deficient animals was determined once. Figure B shows 1 representative experiment of 2 with similar results.
Summary M. tuberculosis H37Rv Δ upk

A upk deletion mutant (M. tuberculosisΔupk) was generated on a M. tuberculosis H37Rv background. In vitro growth properties of the mutant in shaking culture in 7H9 complete medium, cording, and neutral red to staining of this strain were unaffected. In addition, standing cultures in Sauton medium exhibited impaired pellicle formation. Global analysis of proteome and transcriptome revealed a high number of genes associated with lipid metabolism upregulated in the mutant, especially an operon of the mycobacterial FAS-II system. Increased sensitivity to bacitracin, however, was not detected. The upk deficient M. tuberculosis strain exhibited markedly reduced growth and pathology in vivo as well as reduced virulence in Rag1^-/- and IFNγ^-/- KO mice infections.

M. bovis BCG Δupk Infection studies

Balb/c mice were infected with 5 x 10⁵ cfu of the M. bovis BCG Δupk strain and the M. bovis BCG wildtype strain i.v. and bacterial numbers were determined at days 15, 30, 60, and 90 post infection in lung and liver (Fig. 28). In the median, the bacterial burden in the lung of M. bovis BCG wildtype infected mice was about 2.17 times higher compared to mice infected with the upk deletion mutant, and 8.2 times higher in the liver. The small difference in bacterial load remained almost constant over the observed period of 90 days but was not significant according to “Mann Whitney” test (lung P = 0.5; liver P = 0.2).

Fig. 28 Growth of wildtype and upk-deficient M. bovis BCG in lung and liver of Balb/C mice infected with 5 x 10⁵ CFU. Filled squares represent cfu of wildtype M. bovis BCG, and open squares represent cfu of the M. bovis BCG upk deletion mutant. At each time-point 5 mice per group were sacrificed.
IFN γ production of stimulated spleen cells

IFNγ production by spleen cells of infected and of non infected mice was addressed by ELISA-assay (Fig. 29). Cells of whole spleens were either stimulated or left unstimulated with M. tuberculosis protein extracts. Spleen cells derived from naive mice failed to produce IFNγ, whilst cells of M. bovis BCG wildtype infected mice produced high levels of IFNγ at day 60 and day 90 post infection. Delayed IFNγ production of a comparably high level was measured at day 90 post infection in the case of spleen cells derived from mice infected with the BCG Δupk deletion mutant.

Fig. 29 Measurement of IFNγ production by ELISA. Spleen cells of M. bovis BCG inoculated mice produced high levels of IFNγ upon stimulation at day 60 and 90 post infection. Within each group, left column displays unstimulated, right column displays stimulated samples. Spleen cells of mice vaccinated with upk deficient M. bovis BCG strain produced a delayed but also high response at day 90 post infection.
Vaccine trial
A major goal of studies with recombinant M. bovis BCG would be their utilization as improved vaccines. To exploit this possibility we compared vaccine efficacy of M. bovis BCG Δupk to the existing vaccine M. bovis BCG. Balb/c mice were vaccinated i.v. with 5 x 105 cfu. After 120 days these animals and an unvaccinated control group were challenged with about 200 cfu M. tuberculosis H37Rv delivered as aerosol. At distinct time-points thereafter, bacterial loads in lung and spleen were determined (Fig. 30). M. tuberculosis cfu differences in the spleen were very small between the groups 30, 60, and 120 days post infection. The M. tuberculosis burden in the lung of both groups of vaccinated animals was about the same and 60 fold lower compared to unvaccinated animals at day 30 post infection. However, by day 120 post infection, the BCG Δupk mutant strain was able to induce a significantly superior protection (Δlog = 2.7 in relation to naive mice) compared to wildtype M. bovis BCG (Δlog = 0.9) in the lung.

Fig. 30 Bacterial burden of Balb/c micechallenged with M. tuberculosis H37Rv viaaerosol. Filled squares represent M. tuberculosis cfu of wildtype M. bovis BCG vaccinated animals, open squares represent M. tuberculosis cfu of the M. bovis BCG Δupk vaccinated animals, crosses represent M. tuberculosis cfu of unvaccinated animals.

According to Mann Whitney test, bacterial numbers of M. bovis BCG and the M. bovis BCG Δupk mutant were significantly different at day 60 and 120 in the lung (P<0.0001).
Summary M. bovis BCG Δ upk

Mice infected with the M. bovis BCG Δupk strain exhibited lower bacterial load in lung and liver compared to mice infected with wildtype BCG. As a consequence, a delayed IFNγ response was observed. Protection against M. tuberculosis challenge induced by the BCG Δupk mutant strain was highly improved in the lung of vaccinated animals at day 120 post infection compared to animals vaccinated with M. bovis BCG wildtype.