Differential transcriptome of MAP under acid-nitrosative multi-stress
The whole transcriptome of MAP that has been highlighted during the acid-nitrosative stress (Figure ) was defined by an up-regulation of 510 genes ( Additional file 1
: Table S1) and a down-regulation of 478 genes ( Additional file 1
: Table S2) for a total of 988 genes differentially expressed compared to the untreated strain. Transcriptional profile has been grouped into different types of metabolic patterns according to five functional class: intermediate metabolism, energy metabolism, cell wall & membrane, information metabolism and cell processes.
Figure 1 Schematic diagram of MAP transcriptional response during acid-nitrosative multistress. Differentially expressed genes during multi-stress were grouped based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) classification and sorted by function. Up (more ...)
Within the intermediate metabolism category, the subgroup of amino acid metabolism is characterized by a significant up-regulation of the anabolic profile of several amino acids, such as branched-chain amino acids with subunits of acetolactate synthase 2 (MAP4208, MAP3000c, MAP0649), and specifically leucine (leuA) as well as an up-regulation of genes involved in the synthesis of aromatic amino acids (aroK) or specifically with entries for the synthesis of tryptophan (trpE, trpB) along with tyrA for the synthesis of tyrosine. Additional genes for the synthesis of amino acids are up-regulated, such as ald which is involved in the synthesis of alanine from pyruvate together with dapA, dapB and dapE in the synthesis of lysine, as well as the methionine's synthesis with metA and methionine synthase (MAP3055c). Finally, in the same pattern there is an up-regulation of the synthesis of glutamine (glnA3) and some entries related to the synthesis of arginine (argF, argH).
Multi-stress induces an increase in reserve polysaccharides degradation and in lipid anabolism
During acid-nitrosative stress, MAP up-regulates the catabolism of glycogen (glgX, glgP) along with two glycoside hydrolase 15 (MAP2215, MAP1384c) which cleave the non-reducing terminal of dextrose-based polysaccharide complexes leading to D-glucose release. On the other hand, genes responsible for the synthesis of glycogen are repressed (glgB, glgC) as well as the synthesis of polyhydroxyalkanoic acids (PHAs) with the suppression of poly-beta- hydroxybutyrate polymerase acid synthase (MAP1389).
Regarding lipid metabolism, data show a notable shift towards up-regulation of genes involved in the biosynthesis of lipids rather than in the fatty acids degradation. As a matter of fact, genes for lipid biosynthesis are markedly up-regulated (kas, fabG4, fabD2, desA2) as well as MaoC dehydratase (MAP3479c), 3-oxoacyl-carrier reductase (MAP3507), biotin carboxylase (MAP1701c) and diacylglycerol O-acyltransferase (MAP1156) in the last step of triglycerides synthesis.
In line with this many genes for lipid catabolism are down-regulated. Among repressed entries are AMP-dependent synthetase and ligase (MAP2400, MAP2747, MAP3659) and Acyl-CoA dehydrogenase (fadE1, fadE2, fadE15, fadE12, fadE3, fadE25, MAP2655, MAP2352, MAP0682, MAP2656, MAP2351, MAP1758c, MAP3238) together with entries for enoyl-CoA hydratase (echA7, echA21, echA6, echA12) and the patatin protein (MAP1011), which is involved in the cleavage of fatty acids from membrane lipids, together with the lipolytic enzyme G-D-S-L family (MAP1022c) which is down-regulated as well.
Within the pattern of nucleotide metabolism it is interesting to note an up-regulation of the pyrimidine biosynthetic operon repressor (pyrR), for this reason MAP must make up for the loss of synthesis of pyrimidines through a bypass with thyX, required for the synthesis of dTMP, and dcd which is involved in the production of dUMP. An up-regulation can be observed also for nrdI, employed in the synthesis of deoxyribose and eventually in degrading damaged nucleotides with NUDIX protein (MAP3088c).
With respect to the up-regulation pattern, where a repression of pyr operon was triggered, the pyr system which is involved in the classic synthesis of pyrimidines, coherently appears down-regulated (pyrG, pyrF).
As for the last subclass of intermediary metabolism, represented by the metabolism of vitamins and cofactors, an up-regulation of enzymes required for the synthesis of vitamin B12 was observed with cbiX, which participates in the anaerobic insertion of cobalt into the corrin ring, cobyrinic acid a,c-diamide synthase (MAP3314c), cobW and cobT required for the assembling of the cofactor's nucleotide loop in anaerobic metabolism. The synthesis of molybdopterin appears to be up-regulated (mog, moeB) as well as the synthesis of folate with entries such as aminodeoxychorismate lyase (MAP1079), folE and folP. The synthesis of menaquinone is up-regulated (entC, menE, menC) as well as the heme synthesis (hemE, hemL). Unlike from the up-regulation pattern, genes involved in the synthesis of FMN or FAD are repressed (ribF), in addition to the down-regulation of lipA, involved in the synthesis of lipoate and ribokinase (MAP0876c) in the synthesis of thiamine. Eventually, there is also a down-regulation of the synthesis of ubiquinone (ubiX) together with a suppression of the biotin synthesis (bioB) and coenzyme A synthesis (coaA) along with 5'-phosphate oxidase (MAP3177, MAP3028, MAP2630c, MAP0828) related to the synthesis of vitamin B6.
Stressor conditions induce in MAP an increase in anaerobic respiration and nitrate reduction
The energy metabolism of MAP during the acid-nitrosative stress includes the up-regulation of eno
, which is involved in glycolysis, and some entries of the pyruvate dehydrogenase complex (dlaT, pdhB, lpdA
). However, in this stress experiment, it seems that acetate originates also from the degradation of citrate with citE
which is up-regulated. Furthermore some entries of Krebs cycle are also up-regulated (gltA2icd2, sdhC
) together with some components of the electron transport chain such as NAD(P)H quinone oxidoreductase
), but with a different final electron acceptor than molecular oxygen with the up-regulation of nirD
that reduces nitrite to ammonia and periplasmic nitrate reductase
) for nitrate as a final acceptor [29
]. Alternative to Krebs cycle, but in parallel, MAP up-regulates components of the glyoxylate pathway with two entries such as aceAb
and isocitrate lyase
Conversely, in the down-regulation pattern MAP represses oxidative phosphorylation by attenuating the expression of entries such as atpC, nuoG, qcrB and fumarate reductase / succinate dehydrogenase (MAP0691c) that together describe a repression of aerobic respiration with molecular oxygen as final electron acceptor during this stress.
The metabolism of transport in acid-nitrosative stress is represented by an up-regulation of genes involved in the uptake of cobalt such as cobalt / nickel transport system permease protein
) and sulfonate / nitrate / taurine transport system permease protein
) required for the transport of nitrate together with the transport of chloride with the up-regulation of chloride channel protein
). During the stress there is an increase in iron storage with the up-regulation of siderophore interacting FAD binding protein
) although with two factors for iron uptake such fecB
. Finally, a factor required for the uptake of carbohydrates such as mannitol dehydrogenase
) which belongs to the phosphotransferase system (PTS) [30
] is up-regulated.
Acid-nitrosative stress increases the expression of factors for the construction of lipid and glycan components of bacterial cell wall
Several genes involved in cell wall construction are up-regulated (murA, murE, fbpC2
) along with S-layer domain protein
) for the assembly of the surface polycrystalline layer of glycoproteins on the top of the lypoglican envelope [31
], D-alanyl-D-alanine carboxypeptidase
) and ErfK / YbiS / YcfS / YnhG family protein
). It is important to note an up-regulation of the lipopolysaccharide (LPS) synthesis (glf, rmlB2, rmlD
). Moreover, among up-regulated genes are glycosyl transferase group 1
), exopolysaccharide biosynthesis tyrosine-protein kinase
) and D,d-heptose 1,7-bisphosphate phosphatase protein
) required for the construction of the the inner core's precursor [32
]. Finally, the biosynthesis of membrane phospholipids appears up-regulated in acid-nitrosative stress with entries such as PA-phosphatase related protein
) together with phosphatidylethanolamine N-methyltransferase
), phospholipid-binding protein
), phospholipid / glycerol acyltransferase
), diacylglycerol kinase
) and psd
It is worth noting that during the acid-nitrosative stress there is a repression of genes involved in the degradation of the cell wall such as carbohydrate-binding protein
), lytic transglycosylase
), required for the degradation of murein in the cell wall recycling process during division and separation [33
], membrane-bound lytic murein transglycosylase
) and finally a couple of transglycosylase domain protein
) together with mannan endo-1,4-beta-mannosidase
). In addition to these, a repression of cell division was inferred, since cell division FtsK / SpoIIIE
) for cytokinetic ring assembly [34
and ATPase involved in chromosome partitioning
) were down-regulated along with a protein of unknown function DUF881
) involved in the division process.
Finally, there is a down-regulation of the synthesis of mycolic acids consistent with the repression of inhA, mmaA4, kasB and methyltransferase type 12 / Cyclopropane-fatty-acyl- phospholipid synthase (MAP3738c) in the synthesis of cyclopropane fatty acids.
MAP triggers an oxidative stress-like response and suppresses the susceptibility to antibiotics during acid-nitrosative multi-stress
The subcategory of the information metabolism during acid-nitrosative stress is characterized by the up-regulation of phoP
recognized as a positive regulator for the phosphate regulon as well as a virulence factor in MTB [35
]. Several transcription factors are up-regulated during the stress such as protein of unknown function YGGT
) thought to be activated in response to hyperosmotic stress [36
], transcriptional regulator CRP / FNR family
) which responds to various stress stimuli such as oxidative stress and nitrosative stress [37
]; interestingly, among up-regulated entries are also sigE,
induced by oxidative stress or during infection of macrophages [38
] and oxyS
as regulator of oxidative stress response that mimics oxyR
]. It is important to note the up-regulation of transcription factors for activating the uptake and catabolism of carbohydrates such as transcriptional regulator, araC family
) along with furB,
a key protein in the control of intracellular iron concentration.
Within the down-regulated transcriptional profile, it is worth noting the suppression of rsbU
which makes possible, through the activation of rsbV
, the release of sigB
factor sequestered by rsbW
], moreover among repressed entries is sigH
that is one of the activators of sigB
. It is interesting to notice that also sigA
, an important sigma factor recognised as differently expressed in other studies [41
] is repressed, along with several transcriptional regulator, merR family
), that can be traced to a general stress of starvation maybe due to a partial stationary phase condition, and several transcriptional regulator, tetR family
(MAP1477c, MAP3052c, MAP2394, MAP0969, MAP3891, MAP2023c, MAP1721c, MAP3689, MAP0179c, MAP2262, MAP4290, MAP2003c
) involved in the suppression of the susceptibility to hydrophobic antibiotics such as tetracycline [44
]. During the stress there is also a down-regulation of transcriptional regulator, arsR family protein
) required for the suppression of resistance to arsenic compounds together with the repressor of the cell wall synthesis cell wall envelope-related protein transcriptional attenuator
). Finally, it is worth noting the repression of whiB4
, which is useful for differentiation and cell division.
The last subgroup of the information metabolism is the signal transduction within which, during acid-nitrosative stress, transduction through kinases is up-regulated with sensor signal transduction histidine kinase
, together with prrB
which is involved in the adaptation to a new environment or to intracellular growth [38
MAP's metabolism of detoxification reveals an up-regulation of detoxification enzymes such as sodC
, which is responsible for the degradation of superoxides, together with katG
for peroxides elimination, as well as arsC
for detoxification from arsenic acid or heavy metals [45
]. It is important to note the up-regulation of the resistance to multiple antibiotics with several entries such as aminoglycoside phosphotransferase
), antibiotic transport system permease protein
) and prolyl 4- hydroxylase, alpha subunit
) in the hydroxylation-mediated inactivation.
Regarding the subgroup of antigenicity and virulence, it is worth noting the up-regulation of PE-PGRS family protein
) and several PPE proteins (MAP0123MAP1516MAP1519MAP2595MAP3185MAP1003c
) thought to be responsible for the antigenic diversity [46
]. Furthermore, several virulence factors required for cell invasion or escape are up-regulated such as hemolysin
) and mce
) together with a couple of cutinase
) perhaps involved in the destruction of the host cell membrane lipids [47
On the other hand, data show the repression of several immunogenic factors (mpt6, esxD, snm4, lprG), all virulence factors but not necessarily immunogenic, suggesting a change in the antigenic profile of the bacterium, not due to a repression of the antigenic diversity, but to an alternative antigenic profile.
The response to acid-nitrosative stress is characterized by the up-regulation of many stress chaperonins (DnaJHsp20GroESGroEL
) for the protein folding along with resistance factors such as acid resistance membrane protein
) for resistance to acids and three entries of acyltransferase 3
) required for peptidoglycan O-acylation in order to increase its resistance [48
]. There is also an up-regulation in the response to DNA damage with the activation of a not-SOS dependent repair system with enduvrA
for the removal of damaged nucleotides [49
], uracil-DNA glycosylase
) and formamidopyrimidine-DNA glycosylase
) specific for oxidized purines [50
]. Lastly, MAP's transcriptome under acid-nitrosative stress shows the repression of few general chaperonins, probably due to stationary phase starvation, such as GroEL2
identified in "stress endurance" response not due to acute stress [51
], as well as the down-regulation of activator of Hsp90 protein family
) and htrA
, a heat shock protein together with proW
for osmotic shock.
Transcriptome of MAP during the infection of THP-1 human macrophages
The transcriptional pattern of MAP after in vitro
infection of the macrophage cell line THP-1 showed a combination of metabolisms () defined by the expression of a total of 455 genes, 171 of which are up-regulated ( Additional file 1
: Table S3) and 284 are down-regulated ( Additional file 1
: Table S4).
Figure 2 Schematic diagram of MAP transcriptional response during THP-1 infection. Differentially expressed genes during cellular infection were grouped based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) classification and sorted by function. Up arrows (more ...)
Within macrophage MAP up-regulates amino acid catabolism, down-regulates amino acid anabolism and inhibits lipid degradation
It is interesting to notice that within the up-regulated framework there is an increased expression of genes involved in the degradation of asparagine (ansA
), glutamate with NAD- glutamate dehydrogenase
) and phenylalanine with mphA
and fumarylacetoacetate hydrolase protein
). Moreover, it is important to note that the catabolism of cysteine is up-regulated with cysteine desulfurase
), which is involved in the removal of sulfur to yield alanine, an important gene in the synthesis of S-based cofactors [52
Differently, according to the down-regulated pattern, there is a clear shift towards the amino acid anabolism. Therefore, the synthesis of histidine is down-regulated with three entries such as hisI, hisD and histidinol-phosphate aminotransferase (MAP4211). Among down-regulated entries are also those required for the synthesis of methionine with four repressed genes such as metC, metH, homocysteine methyltransferase (MAP2279) and lastly cystathione beta-lyase (MAP2055). The synthesis of threonine seems down-regulated (thrC) together with the synthesis of glutamine (glnA2) and lysine with dihydrodipicolinate reductase protein (MAP2013c, MAP3619).
The metabolism of carbohydrates shows during THP-1 infection an up-regulation of lpqI which participates in the hydrolysis of beta-linkages in polysaccharides and the consequently release of free glucose.
The down-regulated profile shows rather the opposite process to the degradation of polysaccharides, although with formation of alpha-linkages, with glgC involved in the synthesis of glycogen.
The lipid metabolism is characterized by a slight up-regulation of the synthesis of fatty acids with fabG2 and MaoC domain protein dehydratase (MAP3479c).
On the other hand during the THP-1 infection, MAP's degradation of lipids is heavily down-regulated with the repression of fadD13, fadE6 and acyl-CoA dehydrogenase (MAP3238), as well as three entries for enoyl-CoA hydratase (echA9, echA19, echA16) and fadA6. Lastly, a gene involved in the degradation of sterols, steroid delta-5-3-ketosteroid isomerase (MAP1773c), is down-regulated.
Intramacrophage environment brings MAP to employ mechanisms for energy production and cofactors biosynthesis through anaerobic pathways
As far as the metabolism of cofactors and vitamins is concerned, among up-regulated genes are those specific for the synthesis of folate such as aminodeoxychorismate lyase protein (MAP1079) and dfrA along with genes responsible for the synthesis of porphyrins (hemE, hemZ) for heme production. In addition, there is an increase in the synthesis of B12 cofactor through anaerobic process (cobT) together with the up-regulation of the synthesis of biotin (bioF) and the biosynthesis of menaquinone (menB).
In opposite to the up-regulation profile, the synthesis of B12 cofactor under aerobic conditions is down-regulated with cobN required for the aerobic synthesis of its corrin ring, along with the the synthesis of coenzyme A with coaA and dephospho-CoA kinase (MAP1326). During THP-1 infection MAP up-regulates acn that is used both in tricarboxylic acid (TCA) cycle and in glyoxylate pathway. In addition there is also an up-regulation of the pentose phosphate pathway with glucose-6-phosphate 1-dehydrogenase (MAP1687).
On the other hand, among down-regulated genes are entries for TCA cycle (gltA1, mdh), as well as several entries for oxidative phosphorylation such as nuoG, ndh and NAD(P)H quinone oxidoreductase (MAP0245c) and ATP synthesis using molecular oxygen as final electron acceptor such as ATP synthase I (MAP2458c) together with atpE.
Intracellular MAP increases the expression of factors related to polypeptides translocation and production of metal chelators
As far as the metabolism of transport is concerned, it is important to note an increase in genes involved in protein translocation with the up-regulation of entries such as secG
and a couple of peptide / nickel transport system permease protein
) along with an up-regulation of factors concerning the transport of chloride such as chloride channel protein
) and the “low-affinity” uptake of phosphate (pitA
] as well as sulfonate / nitrate / taurine transport system permease protein
) involved in the nitrate transport. Finally, it is worth noting how sugB
, which is responsible for sugar transport and uptake, is up-regulated together with entB
required for capturing iron from host cell's iron chelator compounds [54
On the other hand, the down-regulated expression profile shows a repression of the “forced” system of phosphate uptake (phoH, phoT, pstA1_1, pstA1_2) thus showing the repression both in the activation of the pho system and in the induction of the pst system. It is interesting to notice that the down-regulated pattern is also dominated by the repression of the uptake of cationic metals such as nickel (nicT) and molybdenum (modC, modD) and the transport of lipids which is suppressed with mmpL11 and mmpl protein (MAP2233).
Within macrophage MAP up-regulates genes for membrane lipids but not in peptidoglycan biosynthesis
The cell wall and membrane metabolism of MAP during the THP-1 infection is characterized by the up-regulation of genes involved in the synthesis of membrane lipid structures such as LPS with D,d-heptose-1,7-bisphosphate phosphatase protein (MAP3251) as well as entries required for the synthesis of phospholipids such as phospholipid / glycerol acyltransferase (MAP1160c), 1-acyl-sn-glycerol-3-phosphate acyltransferase (MAP1920c), hemolysin (MAP3059c), pgsA2 and pgsA3. Finally, there is also an up-regulation in the production of mycolic acids with fbpC2 that is necessary for the biogenesis of the cord factor.
The down-regulated expression pattern is mainly featured by the suppression of the synthesis of peptidoglycan with genes such as gmdA, murE, murG, murX and bifunctional phosphoglucose / phosphomannose isomerase (MAP3368c). Along with the down-regulation of maf-like protein (MAP3401) responsible for the inhibition of the partitioning septum, thus suggesting a possible increase in cell division.
Intracellular MAP increases the expression of genes involved in antibiotics resistance and radical agents as well as factors for cellular evasion, but not for invasion
Information metabolism is characterized by the up-regulation of genes concerning the regulation of sugar metabolism such as transcriptional regulator, araC family (MAP3758c, MAP1652c) and transcriptional regulator, gntR family (MAP3599c) that regulate the biosynthesis of sugars. The last up-regulated entry is transcriptional regulator, merR family (MAP3267c) which is important for the response to oxidative stress and antibiotics.
Among the down-regulated genes are two sigma factors such as SigI
which is activated in response to general stress and SigJ
, required for the regulation of expression in stationary phase cultures [55
]. The susceptibility to lipophilic antibiotics is repressed since four genes coding for transcriptional regulator, tetR family
) are down-regulated along with the repression of the glyoxylate path with transcriptional regulator, iclR family
With respect to the detoxification metabolism during macrophage infection, MAP up-regulates sodC in order to dismutate superoxides, and increases its antibiotic resistance by up-regulating genes such as aminoglycoside phosphotransferase (MAP3197), prolyl 4-hydroxylase, alpha subunit (MAP1976) and antibiotic transport system permease (MAP3532c) for their efflux.
Virulence and antigenicity of MAP during infection of THP-1 are dominated by the up-regulation of mpt64, tlyA, peptidase M22 glycoprotease (MAP4261), and family PE-PGRS protein (MAP4144).
The hbha gene for host cell adhesion as well as mce1C for the invasion of mammalian host cells are down-regulated, thus limiting the invasive feature of MAP during intramacrophage infection. Lastly, there is a down-regulation of components belonging to antigenic variability such as four PPE family protein (MAP0966c, MAP2927, MAP1515, MAP3737) that are repressed.
The stress metabolism shows an up-regulation of acid-resistance membrane protein (MAP1317c) specific for resistance to acidic environment, uspA (MAP1754c) and two entries for the repair of damaged DNA such as recR and end.
On the other hand, within this metabolism two entries such as Hsp20 and dnaJ are repressed along with domain-containing protein PitT (MAP2680c, MAP2027c) required for MAP's survival under nutritional stress.
Comparison of acid-nitrosative multi-stress and THP-1 infection MAP's transcriptomes
MAP's transcriptome resulting from the acid-nitrosative stress is more complex and rich (n
988) than the detectable transcriptome during infection of the macrophage line THP-1 (n
455). Between the two transcriptomes it is possible to find analogies of up-regulation or down-regulation for several entries since 50 and 24 genes are commonly up-regulated and down-regulated, respectively (Figure ). Homologies can be found in the intermediate metabolism, where there is a repression of the synthesis of glycogen both in the acid- nitrosative stress (glgBglgC
) and in the cellular infection (glgC
), thus highlighting a limitation in extracellular sources of carbohydrates. In the lipid metabolism both transcriptional profiles underline an up-regulation trend towards the lipid synthesis (MAP3479c
) together with a repression of lipid degradation (MAP3238
), in broad agreement with other studies where lipid synthesis was already observed as up-regulated in experiments of multiple-stress in MTB [56
] since they may serve as nutrient storage.
Figure 3 Functional clustering of common regulated MAP genes under acid-nitrosative multi-stress and THP-1 infection. Expression ratios were log2-transformed, and displayed according to the color code at the top of the figure. Venn diagrams showing the number (more ...)
The down-regulation of pyrimidine synthesis is a common repressed metabolism between the acid-nitrosative stress and the infection especially in the first where the synthesis is repressed by the pyrR
regulator resulting in a down-regulation of pyr
genes, perfectly correlated with the same mechanism of genic regulation occurred in previous experiments inherent MTB's response to inhibitors of translation [19
] in which it was shown that the translational inhibition induced the bacterium to trigger a response that included both the repression of de novo
nucleotides synthesis and the increase of the synthesis of ribosomes.
Finally, the situation appears very complex in the common metabolism of synthesis of vitamins and cofactors in which the up-regulation of folate synthesis occurs in both transcriptional profiles with the same entry aminodeoxychorismate lyase protein
) as well as the synthesis of vitamin B12 (cobT
) and the synthesis of porphyrins (hemE
). In this case, the up-regulation of porphyrins synthesis may be due to the situation of starvation that requires MAP to shift its energy metabolism from an aerobic condition to an anaerobic state using enzymes that cooperate with ferredoxines in the transfer of electrons in redox reactions as like as a metabolism pattern already identified in previous studies with the induction of slow growth and hypoxic cultures of Mycobacterium smegmatis
Further evidences about the switch of energy metabolism from aerobic pathway to anaerobic conditions are represented by the common up-regulation of the synthesis of menaquinone in both experiments, respectively with menA
in acid-nitrosative stress and in the cellular infection, since it could be an essential factor for the survival of non-replicating mycobacteria [58
], thus corroborating the decrease of cell multiplication given by the down-regulation of functional genes for cell division. The only homology in the down-regulation profile of metabolism of cofactors is the repression of coaA,
probably in line with the down-regulation of lipid degradation.
As far as the energy metabolism is concerned, both transcriptomes are characterized by the up-regulation of the glyoxylate pathway in particular in the acid-nitrosative stress with aceAb
, which was identified in many works as a factor expressed by mycobacteria to survive inside the macrophage and in other infection models as well as during growth with lipids as the sole sources of carbon [59
]. Nevertheless, the up-regulation of genes involved in the synthesis of lipids, especially in the construction of lipid membrane structures, is in contrast with previous works reporting that inside the macrophage mycobacteria, such as MTB, shifted their energy metabolism to the use of fatty acids in beta-oxidation [24
However, the regime of anaerobic respiration is further confirmed by the down-regulation of oxidative phosphorylation both for subunits of NADH dehydrogenase
and for other complexes involved in electron transport chain together with F0F1 ATPase
subunits as already observed in experiments with MTB under nutrient starvation [60
], oxidative agents [61
] and in infection of macrophages [62
] in addition to the common down-regulation of nuoG,
which was identified in MTB as an antiapoptotic factor for macrophages [63
In the complex metabolism of cell wall and membrane, both transcriptomes show a common up-regulation of the synthesis of LPS (MAP3251
) and membrane phospholipids (MAP3059c
) while in the cell processing metabolism, a common up-regulation of resistance factors to multiple antibiotics (MAP3197MAP1976MAP3532c
), together with a common down-regulation of some tetR
) involved in the suppression of the resistance to lipophilic antibiotics, is consistently present as similarly seen in MTB with multiple stress experiments [56
]. Additionally, the detoxification metabolism underlines a common degradation pathway for reactive oxygen species with sodC
which was also found to be significantly expressed in MTB during oxidative stress [61
] together with the up-regulation of acid-resistance membrane protein
) in order to cope with the acidic environment, and end
required for the repair of DNA damage, previously identified in MTB after treatment with antibacterial agents [64
]. Finally, MAP's virulence exhibits a common up-regulation of the PE-PGRS family protein
) in both transcriptomes which might be a common response to the antigenic diversity profile.