Amit Singh | IIT Patna (original) (raw)
Papers by Amit Singh
Proceedings of The National Academy of Sciences, 2006
The sudden increase in information derived from the completed Mycobacterium tuberculosis (Mtb) ge... more The sudden increase in information derived from the completed Mycobacterium tuberculosis (Mtb) genome sequences has revealed the need for approaches capable of converting raw genome sequence data into functional information. To date, an experimental system for studying protein-protein association in mycobacteria is not available. We have developed a simple system, termed mycobacterial protein fragment complementation (M-PFC), that is based upon the functional reconstitution of two small murine dihydrofolate reductase domains independently fused to two interacting proteins. Using M-PFC, we have successfully demonstrated dimerization of yeast GCN4, interaction between Mtb KdpD and KdpE, and association between Esat-6 and Cfp-10. We established the association between the sensor kinase, DevS, and response regulator, DevR, thereby demonstrating the potential of M-PFC to study protein associations in the mycobacterial membrane. To validate our system, we screened an Mtb library for proteins that associate with the secreted antigen Cfp-10 and consistently identified Esat-6 in our screens. Additional proteins that specifically associate with Cfp-10 include Rv0686 and Rv2151c (FtsQ), a component and substrate, respectively, of the evolutionary conserved signal recognition pathway; and Rv3596c (ClpC1), an AAA-ATPase chaperone involved in protein translocation and quality control. Our results provide empirical evidence that directly links the Mtb specialized secretion pathway with the evolutionary conserved signal recognition and SecA͞SecYEG pathways, suggesting they share secretory components. We anticipate that M-PFC will be a major contributor to the systematic assembly of mycobacterial protein interaction maps that will lead to the development of better strategies for the control of tuberculosis.
Journal of Bacteriology, 2005
Protein kinases have a diverse array of functions in bacterial physiology, with a distinct role i... more Protein kinases have a diverse array of functions in bacterial physiology, with a distinct role in the regulation of development, stress responses, and pathogenicity. pknF, one of the 11 kinases of Mycobacterium tuberculosis, encodes an autophosphorylating, transmembrane serine/threonine protein kinase, which is absent in the fast-growing, nonpathogenic Mycobacterium smegmatis. Herein, we investigate the physiological role of PknF using an antisense strategy with M. tuberculosis and expressing PknF and its kinase mutant (K41M) in M. smegmatis. Expression of PknF in M. smegmatis led to reduction in the growth rate and shortening and swelling of cells with constrictions. Interestingly, an antisense strain of M. tuberculosis expressing a low level of PknF displayed fast growth and a deformed cell morphology compared to the wild-type strain. Electron microscopy showed that most of the cells of the antisense strain were of a smaller size with an aberrant septum. Furthermore, nutrient transport analysis of these strains was conducted using 3 H-labeled and 14 C-labeled substrates. A significant increase in the uptake of D-glucose but not of glycerol, leucine, or oleic acid was observed in the antisense strain compared to the wild-type strain. The results suggest that PknF plays a direct/indirect role in the regulation of glucose transport, cell growth, and septum formation in M. tuberculosis.
Fems Microbiology Letters, 2003
Corrigendum to ''mymA operon of Mycobacterium tuberculosis: its regulation and importance in the ... more Corrigendum to ''mymA operon of Mycobacterium tuberculosis: its regulation and importance in the cell envelope''
Journal of Bacteriology, 2005
Recently developed 3D time-of-flight cameras have an enormous potential for mobile robotic applic... more Recently developed 3D time-of-flight cameras have an enormous potential for mobile robotic applications in particular for mapping and navigation tasks. This paper presents a new approach for online adaptation of different camera parameters to environment dynamics. These adaptations allow the usage of state-of-the-art 3D cameras reliably in real world environments and enable capturing of 3D scenes with up to 30 frames per second. The performance of the approach is evaluated with respect to different robotic specific tasks in changing environments. A video, showing the performance of the approach, is available at [1].
Proceedings of The National Academy of Sciences, 2006
The sudden increase in information derived from the completed Mycobacterium tuberculosis (Mtb) ge... more The sudden increase in information derived from the completed Mycobacterium tuberculosis (Mtb) genome sequences has revealed the need for approaches capable of converting raw genome sequence data into functional information. To date, an experimental system for studying protein-protein association in mycobacteria is not available. We have developed a simple system, termed mycobacterial protein fragment complementation (M-PFC), that is based upon the functional reconstitution of two small murine dihydrofolate reductase domains independently fused to two interacting proteins. Using M-PFC, we have successfully demonstrated dimerization of yeast GCN4, interaction between Mtb KdpD and KdpE, and association between Esat-6 and Cfp-10. We established the association between the sensor kinase, DevS, and response regulator, DevR, thereby demonstrating the potential of M-PFC to study protein associations in the mycobacterial membrane. To validate our system, we screened an Mtb library for proteins that associate with the secreted antigen Cfp-10 and consistently identified Esat-6 in our screens. Additional proteins that specifically associate with Cfp-10 include Rv0686 and Rv2151c (FtsQ), a component and substrate, respectively, of the evolutionary conserved signal recognition pathway; and Rv3596c (ClpC1), an AAA-ATPase chaperone involved in protein translocation and quality control. Our results provide empirical evidence that directly links the Mtb specialized secretion pathway with the evolutionary conserved signal recognition and SecA͞SecYEG pathways, suggesting they share secretory components. We anticipate that M-PFC will be a major contributor to the systematic assembly of mycobacterial protein interaction maps that will lead to the development of better strategies for the control of tuberculosis.
Journal of Bacteriology, 2005
Protein kinases have a diverse array of functions in bacterial physiology, with a distinct role i... more Protein kinases have a diverse array of functions in bacterial physiology, with a distinct role in the regulation of development, stress responses, and pathogenicity. pknF, one of the 11 kinases of Mycobacterium tuberculosis, encodes an autophosphorylating, transmembrane serine/threonine protein kinase, which is absent in the fast-growing, nonpathogenic Mycobacterium smegmatis. Herein, we investigate the physiological role of PknF using an antisense strategy with M. tuberculosis and expressing PknF and its kinase mutant (K41M) in M. smegmatis. Expression of PknF in M. smegmatis led to reduction in the growth rate and shortening and swelling of cells with constrictions. Interestingly, an antisense strain of M. tuberculosis expressing a low level of PknF displayed fast growth and a deformed cell morphology compared to the wild-type strain. Electron microscopy showed that most of the cells of the antisense strain were of a smaller size with an aberrant septum. Furthermore, nutrient transport analysis of these strains was conducted using 3 H-labeled and 14 C-labeled substrates. A significant increase in the uptake of D-glucose but not of glycerol, leucine, or oleic acid was observed in the antisense strain compared to the wild-type strain. The results suggest that PknF plays a direct/indirect role in the regulation of glucose transport, cell growth, and septum formation in M. tuberculosis.
Fems Microbiology Letters, 2003
Corrigendum to ''mymA operon of Mycobacterium tuberculosis: its regulation and importance in the ... more Corrigendum to ''mymA operon of Mycobacterium tuberculosis: its regulation and importance in the cell envelope''
Journal of Bacteriology, 2005
Recently developed 3D time-of-flight cameras have an enormous potential for mobile robotic applic... more Recently developed 3D time-of-flight cameras have an enormous potential for mobile robotic applications in particular for mapping and navigation tasks. This paper presents a new approach for online adaptation of different camera parameters to environment dynamics. These adaptations allow the usage of state-of-the-art 3D cameras reliably in real world environments and enable capturing of 3D scenes with up to 30 frames per second. The performance of the approach is evaluated with respect to different robotic specific tasks in changing environments. A video, showing the performance of the approach, is available at [1].