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Comparative Proteomic Analysis of Aminoglycosides Resistant and Susceptible Mycobacterium tuberculosis Clinical Isolates for Exploring Potential Drug Targets.

Sharma D, Kumar B, Lata M, Joshi B, Venkatesan K, Shukla S, Bisht D - PLoS ONE (2015)

Bottom Line: Membrane and membrane associated proteins have an anticipated role in biological processes and pathogenesis and are potential targets for the development of new diagnostics/vaccine/therapeutics.Twelve proteins were found to have increased intensities (PDQuest Advanced Software) in resistant isolates and were identified as ATP synthase subunit alpha (Rv1308), Trigger factor (Rv2462c), Dihydrolipoyl dehydrogenase (Rv0462), Elongation factor Tu (Rv0685), Transcriptional regulator MoxR1(Rv1479), Universal stress protein (Rv2005c), 35kDa hypothetical protein (Rv2744c), Proteasome subunit alpha (Rv2109c), Putative short-chain type dehydrogenase/reductase (Rv0148), Bacterioferritin (Rv1876), Ferritin (Rv3841) and Alpha-crystallin/HspX (Rv2031c).Besides that Rv1876, Rv3841 and Rv0685 were found to be associated with iron regulation signifying the role of iron in resistance.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra, India.

ABSTRACT
Aminoglycosides, amikacin (AK) and kanamycin (KM) are second line anti-tuberculosis drugs used to treat tuberculosis (TB) and resistance to them affects the treatment. Membrane and membrane associated proteins have an anticipated role in biological processes and pathogenesis and are potential targets for the development of new diagnostics/vaccine/therapeutics. In this study we compared membrane and membrane associated proteins of AK and KM resistant and susceptible Mycobacterium tuberculosis isolates by 2DE coupled with MALDI-TOF/TOF-MS and bioinformatic tools. Twelve proteins were found to have increased intensities (PDQuest Advanced Software) in resistant isolates and were identified as ATP synthase subunit alpha (Rv1308), Trigger factor (Rv2462c), Dihydrolipoyl dehydrogenase (Rv0462), Elongation factor Tu (Rv0685), Transcriptional regulator MoxR1(Rv1479), Universal stress protein (Rv2005c), 35kDa hypothetical protein (Rv2744c), Proteasome subunit alpha (Rv2109c), Putative short-chain type dehydrogenase/reductase (Rv0148), Bacterioferritin (Rv1876), Ferritin (Rv3841) and Alpha-crystallin/HspX (Rv2031c). Among these Rv2005c, Rv2744c and Rv0148 are proteins with unknown functions. Docking showed that both drugs bind to the conserved domain (Usp, PspA and SDR domain) of these hypothetical proteins and GPS-PUP predicted potential pupylation sites within them. Increased intensities of these proteins and proteasome subunit alpha might not only be neutralized/modulated the drug molecules but also involved in protein turnover to overcome the AK and KM resistance. Besides that Rv1876, Rv3841 and Rv0685 were found to be associated with iron regulation signifying the role of iron in resistance. Further research is needed to explore how these potential protein targets contribute to resistance of AK and KM.

No MeSH data available.


Related in: MedlinePlus

3D model of hypothetical proteins & ferritin showing docking with AK & KM: A1 and A2 shows molecular docking of Rv0148 with AM (red) & KM (blue) respectively, orange color shows SDR domain, yellow color shows interacting residues of SDR domain.B1 and B2 shows molecular docking of Rv2005c with AM (red) & KM (blue) respectively, orange color shows Usp domain, yellow color shows interacting residues of Usp domain. C1 and C2 shows docking of Rv2744c with AM (red) & KM (blue) respectively, orange color shows PspA domain of hypothetical protein, yellow color shows interacting residues of PspA domain. D1 and D2 shows docking of Rv3841 with AM (red) & KM (blue) respectively, orange color shows conserved ferritin domain of protein, yellow color shows interacting residues of conserved ferritin domain, purple color shows interacting residues of unknown domain.
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pone.0139414.g003: 3D model of hypothetical proteins & ferritin showing docking with AK & KM: A1 and A2 shows molecular docking of Rv0148 with AM (red) & KM (blue) respectively, orange color shows SDR domain, yellow color shows interacting residues of SDR domain.B1 and B2 shows molecular docking of Rv2005c with AM (red) & KM (blue) respectively, orange color shows Usp domain, yellow color shows interacting residues of Usp domain. C1 and C2 shows docking of Rv2744c with AM (red) & KM (blue) respectively, orange color shows PspA domain of hypothetical protein, yellow color shows interacting residues of PspA domain. D1 and D2 shows docking of Rv3841 with AM (red) & KM (blue) respectively, orange color shows conserved ferritin domain of protein, yellow color shows interacting residues of conserved ferritin domain, purple color shows interacting residues of unknown domain.

Mentions: Molecular docking analysis of selected 3D models (showing less than 2% discrepancy from Ramachandran plot) of hypothetical proteins was performed to detect their binding with AK and KM. Parameters used for selection of 3D models and molecular docking are represented in Table 5. Docking of Rv0148 and Rv2005c (Fig 3) showed the interaction of both drugs into the central cavity of conserved motif of SDR domain and Usp domain of hypothetical proteins respectively. Interacting residues were almost common for both drugs, which suggests similar binding site for both. Docking with Rv2744c show that both drugs interact at the similar interacting residue of conserved PspA domain of hypothetical protein. With Rv3841 both drugs interacted with amino acids of conserved ferritin domain as well as domain of unknown function.


Comparative Proteomic Analysis of Aminoglycosides Resistant and Susceptible Mycobacterium tuberculosis Clinical Isolates for Exploring Potential Drug Targets.

Sharma D, Kumar B, Lata M, Joshi B, Venkatesan K, Shukla S, Bisht D - PLoS ONE (2015)

3D model of hypothetical proteins & ferritin showing docking with AK & KM: A1 and A2 shows molecular docking of Rv0148 with AM (red) & KM (blue) respectively, orange color shows SDR domain, yellow color shows interacting residues of SDR domain.B1 and B2 shows molecular docking of Rv2005c with AM (red) & KM (blue) respectively, orange color shows Usp domain, yellow color shows interacting residues of Usp domain. C1 and C2 shows docking of Rv2744c with AM (red) & KM (blue) respectively, orange color shows PspA domain of hypothetical protein, yellow color shows interacting residues of PspA domain. D1 and D2 shows docking of Rv3841 with AM (red) & KM (blue) respectively, orange color shows conserved ferritin domain of protein, yellow color shows interacting residues of conserved ferritin domain, purple color shows interacting residues of unknown domain.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4593609&req=5

pone.0139414.g003: 3D model of hypothetical proteins & ferritin showing docking with AK & KM: A1 and A2 shows molecular docking of Rv0148 with AM (red) & KM (blue) respectively, orange color shows SDR domain, yellow color shows interacting residues of SDR domain.B1 and B2 shows molecular docking of Rv2005c with AM (red) & KM (blue) respectively, orange color shows Usp domain, yellow color shows interacting residues of Usp domain. C1 and C2 shows docking of Rv2744c with AM (red) & KM (blue) respectively, orange color shows PspA domain of hypothetical protein, yellow color shows interacting residues of PspA domain. D1 and D2 shows docking of Rv3841 with AM (red) & KM (blue) respectively, orange color shows conserved ferritin domain of protein, yellow color shows interacting residues of conserved ferritin domain, purple color shows interacting residues of unknown domain.
Mentions: Molecular docking analysis of selected 3D models (showing less than 2% discrepancy from Ramachandran plot) of hypothetical proteins was performed to detect their binding with AK and KM. Parameters used for selection of 3D models and molecular docking are represented in Table 5. Docking of Rv0148 and Rv2005c (Fig 3) showed the interaction of both drugs into the central cavity of conserved motif of SDR domain and Usp domain of hypothetical proteins respectively. Interacting residues were almost common for both drugs, which suggests similar binding site for both. Docking with Rv2744c show that both drugs interact at the similar interacting residue of conserved PspA domain of hypothetical protein. With Rv3841 both drugs interacted with amino acids of conserved ferritin domain as well as domain of unknown function.

Bottom Line: Membrane and membrane associated proteins have an anticipated role in biological processes and pathogenesis and are potential targets for the development of new diagnostics/vaccine/therapeutics.Twelve proteins were found to have increased intensities (PDQuest Advanced Software) in resistant isolates and were identified as ATP synthase subunit alpha (Rv1308), Trigger factor (Rv2462c), Dihydrolipoyl dehydrogenase (Rv0462), Elongation factor Tu (Rv0685), Transcriptional regulator MoxR1(Rv1479), Universal stress protein (Rv2005c), 35kDa hypothetical protein (Rv2744c), Proteasome subunit alpha (Rv2109c), Putative short-chain type dehydrogenase/reductase (Rv0148), Bacterioferritin (Rv1876), Ferritin (Rv3841) and Alpha-crystallin/HspX (Rv2031c).Besides that Rv1876, Rv3841 and Rv0685 were found to be associated with iron regulation signifying the role of iron in resistance.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra, India.

ABSTRACT
Aminoglycosides, amikacin (AK) and kanamycin (KM) are second line anti-tuberculosis drugs used to treat tuberculosis (TB) and resistance to them affects the treatment. Membrane and membrane associated proteins have an anticipated role in biological processes and pathogenesis and are potential targets for the development of new diagnostics/vaccine/therapeutics. In this study we compared membrane and membrane associated proteins of AK and KM resistant and susceptible Mycobacterium tuberculosis isolates by 2DE coupled with MALDI-TOF/TOF-MS and bioinformatic tools. Twelve proteins were found to have increased intensities (PDQuest Advanced Software) in resistant isolates and were identified as ATP synthase subunit alpha (Rv1308), Trigger factor (Rv2462c), Dihydrolipoyl dehydrogenase (Rv0462), Elongation factor Tu (Rv0685), Transcriptional regulator MoxR1(Rv1479), Universal stress protein (Rv2005c), 35kDa hypothetical protein (Rv2744c), Proteasome subunit alpha (Rv2109c), Putative short-chain type dehydrogenase/reductase (Rv0148), Bacterioferritin (Rv1876), Ferritin (Rv3841) and Alpha-crystallin/HspX (Rv2031c). Among these Rv2005c, Rv2744c and Rv0148 are proteins with unknown functions. Docking showed that both drugs bind to the conserved domain (Usp, PspA and SDR domain) of these hypothetical proteins and GPS-PUP predicted potential pupylation sites within them. Increased intensities of these proteins and proteasome subunit alpha might not only be neutralized/modulated the drug molecules but also involved in protein turnover to overcome the AK and KM resistance. Besides that Rv1876, Rv3841 and Rv0685 were found to be associated with iron regulation signifying the role of iron in resistance. Further research is needed to explore how these potential protein targets contribute to resistance of AK and KM.

No MeSH data available.


Related in: MedlinePlus