Publications by authors named "Jaydip Ghosh"

10 Publications

  • Page 1 of 1

A Possible Role of the Full-Length Nascent Protein in Post-Translational Ribosome Recycling.

PLoS One 2017 18;12(1):e0170333. Epub 2017 Jan 18.

Department of Biophysics, Molecular Biology and Bioinformatics, University College of Science, University of Calcutta, Kolkata, India.

Each cycle of translation initiation in bacterial cell requires free 50S and 30S ribosomal subunits originating from the post-translational dissociation of 70S ribosome from the previous cycle. Literature shows stable dissociation of 70S from model post-termination complexes by the concerted action of Ribosome Recycling Factor (RRF) and Elongation Factor G (EF-G) that interact with the rRNA bridge B2a/B2b joining 50S to 30S. In such experimental models, the role of full-length nascent protein was never considered seriously. We observed relatively slow release of full-length nascent protein from 50Sof post translation ribosome, and in that process, its toe prints on the rRNA in vivo and in in vitro translation with E.coli S30 extract. We reported earlier that a number of chemically unfolded proteins like bovine carbonic anhydrase (BCA), lactate dehydrogenase (LDH), malate dehydrogenase (MDH), lysozyme, ovalbumin etc., when added to free 70Sin lieu of the full length nascent proteins, also interact with identical RNA regions of the 23S rRNA. Interestingly the rRNA nucleotides that slow down release of the C-terminus of full-length unfolded protein were found in close proximity to the B2a/B2b bridge. It indicated a potentially important chemical reaction conserved throughout the evolution. Here we set out to probe that conserved role of unfolded protein conformation in splitting the free or post-termination 70S. How both the RRF-EFG dependent and the plausible nascent protein-EFG dependent ribosome recycling pathways might be relevant in bacteria is discussed here.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0170333PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5242463PMC
August 2017

A one-pot three-component reaction involving 2-aminochromone in aqueous micellar medium: a green synthesis of hexahydrochromeno[2,3-b]quinolinedione.

Mol Divers 2015 Aug 11;19(3):541-9. Epub 2015 Mar 11.

Department of Chemistry, R. K. Mission Vivekananda Centenary College, Rahara, Kolkata, 700118, West Bengal, India.

An efficient and green synthesis of hitherto unreported 11-(chromen-3-yl)-8,8-dimethyl-8,9-dihydro-6H-chromeno[2,3-b]quinoline-10,12(7H,11H)-dione has been accomplished by a three-component reaction involving 2-aminochromone, chromone-3-carbaldehyde, and 5,5-dimethyl-1,3-cyclohexanedione (dimedone) in 0.5 M aqueous SDS solution. The mechanism of the reaction has been studied by isolating the reaction intermediate. This methodology features eco-friendly reaction conditions, a simple working procedure, high atom-economy and high efficiency in product formation.
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http://dx.doi.org/10.1007/s11030-015-9573-7DOI Listing
August 2015

Involvement of mitochondrial ribosomal proteins in ribosomal RNA-mediated protein folding.

J Biol Chem 2011 Dec 21;286(51):43771-43781. Epub 2011 Oct 21.

Department of Biophysics, Molecular Biology and Bioinformatics, University College of Science, University of Calcutta, Kolkata 700009, India; Department of Biological Sciences, Indian Institute of Science Education and Research, Mohanpur, Nadia 741252, India. Electronic address:

The peptidyl transferase center of the domain V of large ribosomal RNA in the prokaryotic and eukaryotic cytosolic ribosomes acts as general protein folding modulator. We showed earlier that one part of the domain V (RNA1 containing the peptidyl transferase loop) binds unfolded protein and directs it to a folding competent state (FCS) that is released by the other part (RNA2) to attain the folded native state by itself. Here we show that the peptidyl transferase loop of the mitochondrial ribosome releases unfolded proteins in FCS extremely slowly despite its lack of the rRNA segment analogous to RNA2. The release of FCS can be hastened by the equivalent activity of RNA2 or the large subunit proteins of the mitochondrial ribosome. The RNA2 or large subunit proteins probably introduce some allosteric change in the peptidyl transferase loop to enable it to release proteins in FCS.
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http://dx.doi.org/10.1074/jbc.M111.263574DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3243548PMC
December 2011

Growth, cell division and sporulation in mycobacteria.

Antonie Van Leeuwenhoek 2010 Aug 1;98(2):165-77. Epub 2010 May 1.

Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Box 596, 751 24 Uppsala, Sweden.

Bacteria have the ability to adapt to different growth conditions and to survive in various environments. They have also the capacity to enter into dormant states and some bacteria form spores when exposed to stresses such as starvation and oxygen deprivation. Sporulation has been demonstrated in a number of different bacteria but Mycobacterium spp. have been considered to be non-sporulating bacteria. We recently provided evidence that Mycobacterium marinum and likely also Mycobacterium bovis bacillus Calmette-Guérin can form spores. Mycobacterial spores were detected in old cultures and our findings suggest that sporulation might be an adaptation of lifestyle for mycobacteria under stress. Here we will discuss our current understanding of growth, cell division, and sporulation in mycobacteria.
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http://dx.doi.org/10.1007/s10482-010-9446-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2906719PMC
August 2010

Sporulation in mycobacteria.

Proc Natl Acad Sci U S A 2009 Jun 16;106(26):10781-6. Epub 2009 Jun 16.

Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Uppsala SE-751 24, Sweden.

Mycobacteria owe their success as pathogens to their ability to persist for long periods within host cells in asymptomatic, latent forms before they opportunistically switch to the virulent state. The molecular mechanisms underlying the transition into dormancy and emergence from it are not clear. Here we show that old cultures of Mycobacterium marinum contained spores that, upon exposure to fresh medium, germinated into vegetative cells and reappeared again in stationary phase via endospore formation. They showed many of the usual characteristics of well-known endospores. Homologues of well-known sporulation genes of Bacillus subtilis and Streptomyces coelicolor were detected in mycobacteria genomes, some of which were verified to be transcribed during appropriate life-cycle stages. We also provide data indicating that it is likely that old Mycobacterium bovis bacillus Calmette-Guérin cultures form spores. Together, our data show sporulation as a lifestyle adapted by mycobacteria under stress and tempt us to suggest this as a possible mechanism for dormancy and/or persistent infection. If so, this might lead to new prophylactic strategies.
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http://dx.doi.org/10.1073/pnas.0904104106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705590PMC
June 2009

Role of the ribosome in protein folding.

Biotechnol J 2008 Aug;3(8):999-1009

Department of Biophysics, Molecular Biology and Genetics, University College of Science, Kolkata, India.

In all organisms, the ribosome synthesizes and folds full length polypeptide chains into active three-dimensional conformations. The nascent protein goes through two major interactions, first with the ribosome which synthesizes the polypeptide chain and holds it for a considerable length of time, and then with the chaperones. Some of the chaperones are found in solution as well as associated to the ribosome. A number of in vitro and in vivo experiments revealed that the nascent protein folds through specific interactions of some amino acids with the nucleotides in the peptidyl transferase center (PTC) in the large ribosomal subunit. The mechanism of this folding differs from self-folding. In this article, we highlight the folding of nascent proteins on the ribosome and the influence of chaperones etc. on protein folding.
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http://dx.doi.org/10.1002/biot.200800098DOI Listing
August 2008

Protein folding by domain V of Escherichia coli 23S rRNA: specificity of RNA-protein interactions.

J Bacteriol 2008 May 29;190(9):3344-52. Epub 2008 Feb 29.

University College of Science, Department of Biophysics, Molecular Biology and Genetics, 92 A.P.C. Road, Kolkata-700009, India.

The peptidyl transferase center, present in domain V of 23S rRNA of eubacteria and large rRNA of plants and animals, can act as a general protein folding modulator. Here we show that a few specific nucleotides in Escherichia coli domain V RNA bind to unfolded proteins and, as shown previously, bring the trapped proteins to a folding-competent state before releasing them. These nucleotides are the same for the proteins studied so far: bovine carbonic anhydrase, lactate dehydrogenase, malate dehydrogenase, and chicken egg white lysozyme. The amino acids that interact with these nucleotides are also found to be specific in the two cases tested: bovine carbonic anhydrase and lysozyme. They are either neutral or positively charged and are present in random coils on the surface of the crystal structure of both the proteins. In fact, two of these amino acid-nucleotide pairs are identical in the two cases. How these features might help the process of protein folding is discussed.
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http://dx.doi.org/10.1128/JB.01800-07DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2347393PMC
May 2008

In vitro protein folding by E. coli ribosome: unfolded protein splitting 70S to interact with 50S subunit.

Biochem Biophys Res Commun 2008 Feb 7;366(2):598-603. Epub 2007 Dec 7.

Department of Biophysics, Molecular Biology and Genetics, University College of Science, 92 A.P.C. Road, Kolkata 700009, India.

Folding of unfolded protein on Escherichia coli 70S ribosome is accompanied by rapid dissociation of the ribosome into 50S and 30S subunits. The dissociation rate of 70S ribosome with unfolded protein is much faster than that caused by combined effect of translation and polypeptide release factors known to be involved in the dissociation of ribosome into subunits. The protein then reaches a "folding competent" state on 50S and is released to take up native conformation by itself. Release before attaining the folding competent state or prevention of release by cross-linking it with ribosome, would not allow the protein to get back to its native conformation.
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http://dx.doi.org/10.1016/j.bbrc.2007.11.143DOI Listing
February 2008

Ribosome-DnaK interactions in relation to protein folding.

Mol Microbiol 2003 Jun;48(6):1679-92

Department of Biophysics, Molecular Biology and Genetics, University of Calcutta, 92 A. P. C. Road, India.

Bacterial ribosomes or their 50S subunit can refold many unfolded proteins. The folding activity resides in domain V of 23S RNA of the 50S subunit. Here we show that ribosomes can also refold a denatured chaperone, DnaK, in vitro, and the activity may apply in the folding of nascent DnaK polypeptides in vivo. The chaperone was unusual as the native protein associated with the 50S subunit stably with a 1:1 stoichiometry in vitro. The binding site of the native protein appears to be different from the domain V of 23S RNA, the region with which denatured proteins interact. The DnaK binding influenced the protein folding activity of domain V modestly. Conversely, denatured protein binding to domain V led to dissociation of the native chaperone from the 50S subunit. DnaK thus appears to depend on ribosomes for its own folding, and upon folding, can rebind to ribosome to modulate its general protein folding activity.
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http://dx.doi.org/10.1046/j.1365-2958.2003.03538.xDOI Listing
June 2003

Mutations in domain V of the 23S ribosomal RNA of Bacillus subtilis that inactivate its protein folding property in vitro.

Nucleic Acids Res 2002 Mar;30(5):1278-85

Department of Biophysics, Molecular Biology and Genetics, University of Calcutta, 92 A.P.C. Road, Calcutta 700 009, India.

The active site of a protein folding reaction is in domain V of the 23S rRNA in the bacterial ribosome and its homologs in other organisms. This domain has long been known as the peptidyl transferase center. Domain V of Bacillus subtilis is split into two segments, the more conserved large peptidyl transferase loop (RNA1) and the rest (RNA2). These two segments together act as a protein folding modulator as well as the complete domain V RNA. A number of site-directed mutations were introduced in RNA1 and RNA2 of B.subtilis, taking clues from reports of these sites being involved in various steps of protein synthesis. For example, sites like G2505, U2506, U2584 and U2585 in Escherichia coli RNA1 region are protected by deacylated tRNA at high Mg2+ concentration and A2602 is protected by amino acyl tRNA when the P site remains occupied already. Mutations A2058G and A2059G in the RNA1 region render the ribosome Ery(r )in E.coli and Lnc(r )in tobacco chloroplast. Sites in P loop G2252 and G2253 in E.coli are protected against modification by the CCA end of the P site bound tRNA. Mutations were introduced in corresponding nucleotides in B.subtilis RNA1 and RNA2 of domain V. The mutants were tested for refolding using unfolded protein binding assays with unfolded carbonic anhydrase. In the protein folding assay, the mutants showed partial to complete loss of this activity. In the filter binding assay for the RNA-refolding protein complex, the mutants showed an extent of protein binding that agreed well with their protein folding activity.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC101228PMC
http://dx.doi.org/10.1093/nar/30.5.1278DOI Listing
March 2002