Anamitra Bhattacharyya - Academia.edu (original) (raw)

Papers by Anamitra Bhattacharyya

to contain 3,294,935 bp distributed over two circular chromosomes sv of 2,117,144 bp and 1,177,78... more to contain 3,294,935 bp distributed over two circular chromosomes sv of 2,117,144 bp and 1,177,787 bp encoding 3,197 ORFs. By using the pE bioinformatics suite ERGO, 2,487 (78%) ORFs were assigned func- Bi tions. The origins of replication of the two chromosomes are similar to those of other a-proteobacteria. Housekeeping genes, including M those involved in DNA replication, transcription, translation, core Dl metabolism, and cell wall biosynthesis, are distributed on both 22 chromosomes. Type I, II, and III secretion systems are absent, but hi genes encoding sec-dependent, sec-independent, and flagella- ca specific type III, type IV, and type V secretion systems as well as ar adhesins, invasins, and hemolysins were identified. Several fea- ca tures of the B. melitensis genome are similar to those of the m symbiotic Sinorhizobium meliloti. fe fr

Journal of Biological Chemistry, 2000

Journal of Biological Chemistry, 1998

We report the identification and cloning of the telomeres of the filamentous fungus, Aspergillus ... more We report the identification and cloning of the telomeres of the filamentous fungus, Aspergillus nidulans. We have identified three classes of cloned chromosomal ends based on the telomere-associated sequences (TASs) and demonstrated that the telomeric repeat sequence is TTAGGG, identical to that found in vertebrates, including humans, and some lower eukaryotes. One category of telomere clones was found to contain internal, variant TAAGGG repeats. The A.nidulans telomeric tract length is strikingly short (4–22 repeats). We demonstrate that telomere length is remarkably stable in different cell types and at altered growth temperatures, suggesting a highly regulated mechanism for length control.

Wehavestudied thestructure andreactivities oftwokinds ofmismatched DNA sequences-unopposed bases,... more Wehavestudied thestructure andreactivities oftwokinds ofmismatched DNA sequences-unopposed bases, orbulges, andmultiple mismatched pairs ofbases. These weregenerated inaconstant sequence environment, inrelatively longDNA fragments, using atechnique based onheteroduplex formation between sequencescloned into single-stranded M13phage. Themismatched sequenceswere studied fromtwopoints ofview, viz 1.Themobility ofthefragments on gelelectrophoresis inpolyacrylamide was studied inorder to examine possible bending oftheDNA duetothepresenceofthemismatch defect. Suchbending wouldconstitute a global effect on theconformation ofthemolecule. 2.Sequences inandaround themismatches werestudied using enzymeandchemical probes ofDNA structure. Thiswouldreveal more local structural effects ofthemismatched sequences. Weobserved that thestructures ofthebulges andthemultiple mismatches appeartobefundamentally differenE. Thebulged sequencesexhibited alarge gelretardation, consistent with asignificant bend...

Ciba Foundation symposium, 1997

The tandemly repeated DNA sequence of telomeres is typically specified by the ribonucleoprotein e... more The tandemly repeated DNA sequence of telomeres is typically specified by the ribonucleoprotein enzyme telomerase. Telomerase copies part of its intrinsic RNA moiety to make one strand of the telomeric repeat DNA. Recent work has led to the concept of a telomere homeostasis system. We have been studying two key physical components of this system: the telomere itself and telomerase. Mutating the template sequence of telomerase RNA caused various phenotypes: (1) mutating specific residues in the ciliate Tetrahymena and two yeasts showed that they are required for critical aspects of telomerase action; (2) certain mutated telomeric sequences caused a previously unreported phenotype, i.e. a strong anaphase block in Tetrahymena micronuclei; and (3) certain template mutations in the telomerase RNA gene of the yeast Kluyveromyces lactis led to unregulated telomere elongation, which in some cases was directly related to loss of binding to K. lactis Rap1p. Using K. lactis carrying alteration...

L'invention concerne une cellule productrice de butanol et un procede de production de butano... more L'invention concerne une cellule productrice de butanol et un procede de production de butanol. Des cellules productrices de butanol comprenant un systeme de synthese de butanol ou des proteines d'exportation de butanol peuvent etre utilisees pour accroitre la production de butanol a partir d'une composition de substrat de carbone.

Biochemical Society Transactions, 1993

Journal of molecular microbiology and biotechnology, 2002

The Archaeon Methanosarcina mazei and related species are of great ecological importance as they ... more The Archaeon Methanosarcina mazei and related species are of great ecological importance as they are the only organisms fermenting acetate, methylamines and methanol to methane, carbon dioxide and ammonia (in case of methylamines). Since acetate is the precursor of 60% of the methane produced on earth these organisms contribute significantly to the production of this greenhouse gas, e.g. in rice paddies. The 4,096,345 base pairs circular chromosome of M. mazei is more than twice as large as the genomes of the methanogenic Archaea currently completely sequenced (Bult et al., 1996; Smith et al., 1997). 3,371 open reading frames (ORFs) were identified. Based on currently available sequence data 376 of these ORFs are Methanosarcina-specific and 1,043 ORFs find their closest homologue in the bacterial domain. 544 of these ORFs reach significant similarity values only in the bacterial domain. They include 56 of the 102 transposases, and proteins involved in gluconeogenesis, proline biosyn...

Methods in Cell Biology, 1999

ABSTRACT Telomeres are specialized structures at the ends of eukaryotic chromosomes that are requ... more ABSTRACT Telomeres are specialized structures at the ends of eukaryotic chromosomes that are required for chromosome stability and the complete replication of linear chromosomes. In ciliates de novo telomere formation is an essential step in a critical developmental stage—the generation of the new macronucleus. Telomerase is a ribonucleoprotein (RNP) reverse transcriptase responsible for the synthesis of telomeric repeats. Telomerase is the only known reverse transcriptase that contains its own template, which is present in the telomerase RNA moiety as an integral part of the RNP complex. The telomerase RNA of Tetrahymena thermophila is a relatively small RNA (159 nucleotides) with a very well-defined secondary structure. Specific residues of the templating domain are copied to produce the G-rich telomeric strand. Ciliates devote significant cellular resources to the maintenance and replication of telomeres due to the large number of macronuclear chromosomes and the relatively small size of each macronuclear chromosome. Consequently, each cell contains an unusually large number of chromosome ends.

European Journal of Biochemistry, 1992

Proceedings of the National Academy of Sciences, 2002

Brucella melitensis is a facultative intracellular bacterial pathogen that causes abortion in goa... more Brucella melitensis is a facultative intracellular bacterial pathogen that causes abortion in goats and sheep and Malta fever in humans. The genome of B. melitensis strain 16M was sequenced and found to contain 3,294,935 bp distributed over two circular chromosomes of 2,117,144 bp and 1,177,787 bp encoding 3,197 ORFs. By using the bioinformatics suite ERGO, 2,487 (78%) ORFs were assigned functions. The origins of replication of the two chromosomes are similar to those of other α-proteobacteria. Housekeeping genes, including those involved in DNA replication, transcription, translation, core metabolism, and cell wall biosynthesis, are distributed on both chromosomes. Type I, II, and III secretion systems are absent, but genes encoding sec -dependent, sec -independent, and flagella-specific type III, type IV, and type V secretion systems as well as adhesins, invasins, and hemolysins were identified. Several features of the B. melitensis genome are similar to those of the symbiotic Sin...

Proceedings of the National Academy of Sciences, 1997

The ribonucleoprotein (RNP) enzyme telomerase is required for replication of eukaryotic chromosom... more The ribonucleoprotein (RNP) enzyme telomerase is required for replication of eukaryotic chromosomal termini. The RNA moiety of telomerase is essential for enzyme function and provides the template for telomeric DNA synthesis. However, the roles of its nontemplate domains have not been explored. Here we demonstrate that a novel interspecies telomerase RNA swap in vivo creates a functional but aberrant telomerase. Telomerase RNA from the ciliate Glaucoma chattoni was expressed in Tetrahymena thermophila cells. The telomerase RNAs from these two species have almost superimposable secondary structures. The template region base sequence is identical in the two RNAs, but elsewhere their sequences differ by 49%. This hybrid telomerase RNP was enzymatically active but added only short stretches of telomeric repeat tracts in vivo and in vitro. This new enzyme also had a strong, aberrant DNA cleavage activity in vitro . Thus, molecular interactions in the RNP involving nontemplate RNA domains...

Proceedings of the National Academy of Sciences, 2007

Biochemically, the syntrophic bacteria constitute the missing link in our understanding of anaero... more Biochemically, the syntrophic bacteria constitute the missing link in our understanding of anaerobic flow of carbon in the biosphere. The completed genome sequence ofSyntrophus aciditrophicusSB, a model fatty acid- and aromatic acid-degrading syntrophic bacterium, provides a glimpse of the composition and architecture of the electron transfer and energy-transducing systems needed to exist on marginal energy economies of a syntrophic lifestyle. The genome contains 3,179,300 base pairs and 3,169 genes where 1,618 genes were assigned putative functions. Metabolic reconstruction of the gene inventory revealed that most biosynthetic pathways of a typical Gram-negative microbe were present. A distinctive feature of syntrophic metabolism is the need for reverse electron transport; the presence of a unique Rnf-type ion-translocating electron transfer complex, menaquinone, and membrane-bound Fe-S proteins with associated heterodisulfide reductase domains suggests mechanisms to accomplish thi...

Proceedings of the National Academy of Sciences, 2002

Xylella fastidiosa ( Xf ) causes wilt disease in plants and is responsible for major economic and... more Xylella fastidiosa ( Xf ) causes wilt disease in plants and is responsible for major economic and crop losses globally. Owing to the public importance of this phytopathogen we embarked on a comparative analysis of the complete genome of Xf pv citrus and the partial genomes of two recently sequenced strains of this species: Xf pv almond and Xf pv oleander , which cause leaf scorch in almond and oleander plants, respectively. We report a reanalysis of the previously sequenced Xf 9a5c (CVC, citrus) strain and the two “gapped” Xf genomes revealing ORFs encoding critical functions in pathogenicity and conjugative transfer. Second, a detailed whole-genome functional comparison was based on the three sequenced Xf strains, identifying the unique genes present in each strain, in addition to those shared between strains. Third, an “ in silico ” cellular reconstruction of these organisms was made, based on a comparison of their core functional subsystems that led to a characterization of their...

Nucleic Acids Research, 2003

to contain 3,294,935 bp distributed over two circular chromosomes sv of 2,117,144 bp and 1,177,78... more to contain 3,294,935 bp distributed over two circular chromosomes sv of 2,117,144 bp and 1,177,787 bp encoding 3,197 ORFs. By using the pE bioinformatics suite ERGO, 2,487 (78%) ORFs were assigned func- Bi tions. The origins of replication of the two chromosomes are similar to those of other a-proteobacteria. Housekeeping genes, including M those involved in DNA replication, transcription, translation, core Dl metabolism, and cell wall biosynthesis, are distributed on both 22 chromosomes. Type I, II, and III secretion systems are absent, but hi genes encoding sec-dependent, sec-independent, and flagella- ca specific type III, type IV, and type V secretion systems as well as ar adhesins, invasins, and hemolysins were identified. Several fea- ca tures of the B. melitensis genome are similar to those of the m symbiotic Sinorhizobium meliloti. fe fr

Journal of Biological Chemistry, 2000

Journal of Biological Chemistry, 1998

We report the identification and cloning of the telomeres of the filamentous fungus, Aspergillus ... more We report the identification and cloning of the telomeres of the filamentous fungus, Aspergillus nidulans. We have identified three classes of cloned chromosomal ends based on the telomere-associated sequences (TASs) and demonstrated that the telomeric repeat sequence is TTAGGG, identical to that found in vertebrates, including humans, and some lower eukaryotes. One category of telomere clones was found to contain internal, variant TAAGGG repeats. The A.nidulans telomeric tract length is strikingly short (4–22 repeats). We demonstrate that telomere length is remarkably stable in different cell types and at altered growth temperatures, suggesting a highly regulated mechanism for length control.

Wehavestudied thestructure andreactivities oftwokinds ofmismatched DNA sequences-unopposed bases,... more Wehavestudied thestructure andreactivities oftwokinds ofmismatched DNA sequences-unopposed bases, orbulges, andmultiple mismatched pairs ofbases. These weregenerated inaconstant sequence environment, inrelatively longDNA fragments, using atechnique based onheteroduplex formation between sequencescloned into single-stranded M13phage. Themismatched sequenceswere studied fromtwopoints ofview, viz 1.Themobility ofthefragments on gelelectrophoresis inpolyacrylamide was studied inorder to examine possible bending oftheDNA duetothepresenceofthemismatch defect. Suchbending wouldconstitute a global effect on theconformation ofthemolecule. 2.Sequences inandaround themismatches werestudied using enzymeandchemical probes ofDNA structure. Thiswouldreveal more local structural effects ofthemismatched sequences. Weobserved that thestructures ofthebulges andthemultiple mismatches appeartobefundamentally differenE. Thebulged sequencesexhibited alarge gelretardation, consistent with asignificant bend...

Ciba Foundation symposium, 1997

The tandemly repeated DNA sequence of telomeres is typically specified by the ribonucleoprotein e... more The tandemly repeated DNA sequence of telomeres is typically specified by the ribonucleoprotein enzyme telomerase. Telomerase copies part of its intrinsic RNA moiety to make one strand of the telomeric repeat DNA. Recent work has led to the concept of a telomere homeostasis system. We have been studying two key physical components of this system: the telomere itself and telomerase. Mutating the template sequence of telomerase RNA caused various phenotypes: (1) mutating specific residues in the ciliate Tetrahymena and two yeasts showed that they are required for critical aspects of telomerase action; (2) certain mutated telomeric sequences caused a previously unreported phenotype, i.e. a strong anaphase block in Tetrahymena micronuclei; and (3) certain template mutations in the telomerase RNA gene of the yeast Kluyveromyces lactis led to unregulated telomere elongation, which in some cases was directly related to loss of binding to K. lactis Rap1p. Using K. lactis carrying alteration...

L'invention concerne une cellule productrice de butanol et un procede de production de butano... more L'invention concerne une cellule productrice de butanol et un procede de production de butanol. Des cellules productrices de butanol comprenant un systeme de synthese de butanol ou des proteines d'exportation de butanol peuvent etre utilisees pour accroitre la production de butanol a partir d'une composition de substrat de carbone.

Biochemical Society Transactions, 1993

Journal of molecular microbiology and biotechnology, 2002

The Archaeon Methanosarcina mazei and related species are of great ecological importance as they ... more The Archaeon Methanosarcina mazei and related species are of great ecological importance as they are the only organisms fermenting acetate, methylamines and methanol to methane, carbon dioxide and ammonia (in case of methylamines). Since acetate is the precursor of 60% of the methane produced on earth these organisms contribute significantly to the production of this greenhouse gas, e.g. in rice paddies. The 4,096,345 base pairs circular chromosome of M. mazei is more than twice as large as the genomes of the methanogenic Archaea currently completely sequenced (Bult et al., 1996; Smith et al., 1997). 3,371 open reading frames (ORFs) were identified. Based on currently available sequence data 376 of these ORFs are Methanosarcina-specific and 1,043 ORFs find their closest homologue in the bacterial domain. 544 of these ORFs reach significant similarity values only in the bacterial domain. They include 56 of the 102 transposases, and proteins involved in gluconeogenesis, proline biosyn...

Methods in Cell Biology, 1999

ABSTRACT Telomeres are specialized structures at the ends of eukaryotic chromosomes that are requ... more ABSTRACT Telomeres are specialized structures at the ends of eukaryotic chromosomes that are required for chromosome stability and the complete replication of linear chromosomes. In ciliates de novo telomere formation is an essential step in a critical developmental stage—the generation of the new macronucleus. Telomerase is a ribonucleoprotein (RNP) reverse transcriptase responsible for the synthesis of telomeric repeats. Telomerase is the only known reverse transcriptase that contains its own template, which is present in the telomerase RNA moiety as an integral part of the RNP complex. The telomerase RNA of Tetrahymena thermophila is a relatively small RNA (159 nucleotides) with a very well-defined secondary structure. Specific residues of the templating domain are copied to produce the G-rich telomeric strand. Ciliates devote significant cellular resources to the maintenance and replication of telomeres due to the large number of macronuclear chromosomes and the relatively small size of each macronuclear chromosome. Consequently, each cell contains an unusually large number of chromosome ends.

European Journal of Biochemistry, 1992

Proceedings of the National Academy of Sciences, 2002

Brucella melitensis is a facultative intracellular bacterial pathogen that causes abortion in goa... more Brucella melitensis is a facultative intracellular bacterial pathogen that causes abortion in goats and sheep and Malta fever in humans. The genome of B. melitensis strain 16M was sequenced and found to contain 3,294,935 bp distributed over two circular chromosomes of 2,117,144 bp and 1,177,787 bp encoding 3,197 ORFs. By using the bioinformatics suite ERGO, 2,487 (78%) ORFs were assigned functions. The origins of replication of the two chromosomes are similar to those of other α-proteobacteria. Housekeeping genes, including those involved in DNA replication, transcription, translation, core metabolism, and cell wall biosynthesis, are distributed on both chromosomes. Type I, II, and III secretion systems are absent, but genes encoding sec -dependent, sec -independent, and flagella-specific type III, type IV, and type V secretion systems as well as adhesins, invasins, and hemolysins were identified. Several features of the B. melitensis genome are similar to those of the symbiotic Sin...

Proceedings of the National Academy of Sciences, 1997

The ribonucleoprotein (RNP) enzyme telomerase is required for replication of eukaryotic chromosom... more The ribonucleoprotein (RNP) enzyme telomerase is required for replication of eukaryotic chromosomal termini. The RNA moiety of telomerase is essential for enzyme function and provides the template for telomeric DNA synthesis. However, the roles of its nontemplate domains have not been explored. Here we demonstrate that a novel interspecies telomerase RNA swap in vivo creates a functional but aberrant telomerase. Telomerase RNA from the ciliate Glaucoma chattoni was expressed in Tetrahymena thermophila cells. The telomerase RNAs from these two species have almost superimposable secondary structures. The template region base sequence is identical in the two RNAs, but elsewhere their sequences differ by 49%. This hybrid telomerase RNP was enzymatically active but added only short stretches of telomeric repeat tracts in vivo and in vitro. This new enzyme also had a strong, aberrant DNA cleavage activity in vitro . Thus, molecular interactions in the RNP involving nontemplate RNA domains...

Proceedings of the National Academy of Sciences, 2007

Biochemically, the syntrophic bacteria constitute the missing link in our understanding of anaero... more Biochemically, the syntrophic bacteria constitute the missing link in our understanding of anaerobic flow of carbon in the biosphere. The completed genome sequence ofSyntrophus aciditrophicusSB, a model fatty acid- and aromatic acid-degrading syntrophic bacterium, provides a glimpse of the composition and architecture of the electron transfer and energy-transducing systems needed to exist on marginal energy economies of a syntrophic lifestyle. The genome contains 3,179,300 base pairs and 3,169 genes where 1,618 genes were assigned putative functions. Metabolic reconstruction of the gene inventory revealed that most biosynthetic pathways of a typical Gram-negative microbe were present. A distinctive feature of syntrophic metabolism is the need for reverse electron transport; the presence of a unique Rnf-type ion-translocating electron transfer complex, menaquinone, and membrane-bound Fe-S proteins with associated heterodisulfide reductase domains suggests mechanisms to accomplish thi...

Proceedings of the National Academy of Sciences, 2002

Xylella fastidiosa ( Xf ) causes wilt disease in plants and is responsible for major economic and... more Xylella fastidiosa ( Xf ) causes wilt disease in plants and is responsible for major economic and crop losses globally. Owing to the public importance of this phytopathogen we embarked on a comparative analysis of the complete genome of Xf pv citrus and the partial genomes of two recently sequenced strains of this species: Xf pv almond and Xf pv oleander , which cause leaf scorch in almond and oleander plants, respectively. We report a reanalysis of the previously sequenced Xf 9a5c (CVC, citrus) strain and the two “gapped” Xf genomes revealing ORFs encoding critical functions in pathogenicity and conjugative transfer. Second, a detailed whole-genome functional comparison was based on the three sequenced Xf strains, identifying the unique genes present in each strain, in addition to those shared between strains. Third, an “ in silico ” cellular reconstruction of these organisms was made, based on a comparison of their core functional subsystems that led to a characterization of their...

Nucleic Acids Research, 2003