Biomedical subjects

Debabrata Biswas

Publications and source records attributed to Debabrata Biswas.

12 recordsLinked to original sources

PubMed2006

Opposing roles for Set2 and yFACT in regulating TBP binding at promoters.

Previous work links histone methylation by Set2 with transcriptional elongation. yFACT (Spt16-Pob3 and Nhp6) reorganizes nucleosomes and functions in both transcriptional initiation and elongation. We show that growth defects caused by spt16 or pob3 mutations can be suppressed by deleting SET2, suggesting that Set2 and yFACT have opposing roles. Set2 methylates K36 of histone H3, and K36 substitutions also suppress yFACT mutations. In contrast, set1 enhances yFACT mutations. Methylation at H3 K4 by Set1 is required for set2 to suppress yFACT defects. We did not detect an elongation defect at an 8 kb ORF in yFACT mutants. Instead, pob3 mutants displayed reduced binding of both pol II and TBP to the GAL1 promoter. Importantly, both GAL1 transcription and promoter binding of pol II and TBP are significantly restored in the pob3 set2 double mutant. Defects caused by an spt16 mutation are enhanced by either TBP or TFIIA mutants. These synthetic defects are suppressed by set2, demonstrating that yFACT and Set2 oppose one another during transcriptional initiation at a step involving DNA binding by TBP and TFIIA.

Amino Acid Substitution↗

PubMed2005

Genetic interactions between Nhp6 and Gcn5 with Mot1 and the Ccr4-Not complex that regulate binding of TATA-binding protein in Saccharomyces cerevisiae.

Our previous work suggests that the Nhp6 HMGB protein stimulates RNA polymerase II transcription via the TATA-binding protein TBP and that Nhp6 functions in the same functional pathway as the Gcn5 histone acetyltransferase. In this report we examine the genetic relationship between Nhp6 and Gcn5 with the Mot1 and Ccr4-Not complexes, both of which have been implicated in regulating DNA binding by TBP. We find that combining either a nhp6ab or a gcn5 mutation with mot1, ccr4, not4, or not5 mutations results in lethality. Combining spt15 point mutations (in TBP) with either mot1 or ccr4 also results in either a growth defect or lethality. Several of these synthetic lethalities can be suppressed by overexpression of TFIIA, TBP, or Nhp6, suggesting that these genes facilitate formation of the TBP-TFIIA-DNA complex. The growth defect of a not5 mutant can be suppressed by a mot1 mutant. HO gene expression is reduced by nhp6ab, gcn5, or mot1 mutations, and the additive decreases in HO mRNA levels in nhp6ab mot1 and gcn5 mot1 strains suggest different modes of action. Chromatin immunoprecipitation experiments show decreased binding of TBP to promoters in mot1 mutants and a further decrease when combined with either nhp6ab or gcn5 mutations.

Adenosine Triphosphatases↗

PubMed2005

The yeast FACT complex has a role in transcriptional initiation.

A crucial step in eukaryotic transcriptional initiation is recognition of the promoter TATA by the TATA-binding protein (TBP), which then allows TFIIA and TFIIB to be recruited. However, nucleosomes block the interaction between TBP and DNA. We show that the yeast FACT complex (yFACT) promotes TBP binding to a TATA box in chromatin both in vivo and in vitro. The SPT16 gene encodes a subunit of yFACT, and we show that certain spt16 mutations are synthetically lethal with TBP mutants. Some of these genetic defects can be suppressed by TFIIA overexpression, strongly suggesting a role for yFACT in TBP-TFIIA complex formation in vivo. Mutations in the TOA2 subunit of TFIIA that disrupt TBP-TFIIA complex formation in vitro are also synthetically lethal with spt16. In some cases this spt16 toa2 lethality is suppressed by overexpression of TBP or the Nhp6 architectural transcription factor that is also a component of yFACT. The Spt3 protein in the SAGA complex has been shown to regulate TBP binding at certain promoters, and we show that some spt16 phenotypes can be suppressed by spt3 mutations. Chromatin immunoprecipitations show TBP binding to promoters is reduced in single spt16 and spt3 mutants but increases in the spt16 spt3 double mutant, reflecting the mutual suppression seen in the genetic assays. Finally, in vitro studies show that yFACT promotes TBP binding to a TATA sequence within a reconstituted nucleosome in a TFIIA-dependent manner. Thus, yFACT functions in establishing transcription initiation complexes in addition to the previously described role in elongation.

Cell Cycle Proteins↗

PubMed2004

Classical projected phase space density of billiards and its relation to the quantum neumann spectrum.

A comparison of classical and quantum evolution usually involves a quasiprobability distribution as a quantum analogue of the classical phase space distribution. In an alternate approach that we adopt here, the classical density is projected on to the configuration space. We show that for billiards, the eigenfunctions of the coarse-grained projected classical evolution operator are identical to a first approximation to the quantum Neumann eigenfunctions. However, even though there exists a correspondence between the respective eigenvalues, their time evolutions differ. This is demonstrated numerically for the stadium and lemon-shaped billiards.

Journal Article↗

PubMed2004

Infection with Campylobacter jejuni induces tyrosine-phosphorylated proteins into INT-407 cells.

The mechanisms used by Campylobacter jejuni to induce internalization into host intestinal epithelial cells have not been defined. In this study, we obtained evidence that exposure of INT-407 cells to protein kinase inhibitors results in decreased invasion of these cells by C. jejuni in a dose dependent manner. Preincubation of INT-407 cells in the presence of staurosporine, tyrphostin 46 and genistein decreased invasion of these cells by C. jejuni significantly. Moreover, C. jejuni infection of INT-407 cells induced tyrosine phosphorylation of several Triton X-100 soluble proteins with approximate molecular weights of 170, 145, 90, 60 and 55 kDa that were absent or reduced in the presence of genistein in cells after 1 hr of pretreatment. These data suggest that tyrosine protein kinase-linked pathways strongly regulate the internalization of C. jejuni into intestinal epithelial cells.

Campylobacter jejuni↗

PubMed2004

A 22-mer primer enhances discriminatory power of AP-PCR fingerprinting technique in characterization of leptospires.

OBJECTIVES: To evaluate the discriminatory power and usefulness of arbitrarily primed-polymerase chain reaction (AP-PCR) characterization of leptospires with M16 primer. METHODS: AP-PCR fingerprints of 20 reference strains of Leptospira representing 20 different serovars belonging to seven genospecies (Leptospira interrogans, 11; L. noguchii, 2; L. borgpetersenii, 1; L. santarosai, 2; L. biflexa, 2; L. kirschneri, 1; L. weilii, 1) were generated by employing M16 primer. Fingerprints generated with this primer were compared with those generated with two other commonly used primers PB1, and L10. An attempt was also made to type 20 leptospiral isolates with the M16 primer. RESULTS AND CONCLUSION: Fingerprints with M16 primer could not only differentiate between strains of different genospecies, but also between strains of the same genospecies belonging to different serovars. While two commonly used primers (PB1 and L10) failed to discriminate between some of the different serovars belonging to the same genospecies, this primer was able to generate discriminatory fingerprints for all strains tested. All 20 Leptospira isolates, recovered from patients in Andaman Islands, could also be typed by fingerprints generated with the M16 primer. The discriminatory power of M16 primer adds more specificity to the rapidity of this system of characterization and can be used as an excellent tool in epidemiological studies on Leptospira.

Base Sequence↗

PubMed2004

Secretion of virulence proteins from Campylobacter jejuni is dependent on a functional flagellar export apparatus.

Campylobacter jejuni, a gram-negative motile bacterium, secretes a set of proteins termed the Campylobacter invasion antigens (Cia proteins). The purpose of this study was to determine whether the flagellar apparatus serves as the export apparatus for the Cia proteins. Mutations were generated in five genes encoding three structural components of the flagella, the flagellar basal body (flgB and flgC), hook (flgE2), and filament (flaA and flaB) genes, as well as in genes whose products are essential for flagellar protein export (flhB and fliI). While mutations that affected filament assembly were found to be nonmotile (Mot-) and did not secrete Cia proteins (S-), a flaA (flaB+) filament mutant was found to be nonmotile but Cia protein secretion competent (Mot-, S+). Complementation of a flaA flaB double mutant with a shuttle plasmid harboring either the flaA or flaB gene restored Cia protein secretion, suggesting that Cia export requires at least one of the two filament proteins. Infection of INT 407 human intestinal cells with the C. jejuni mutants revealed that maximal invasion of the epithelial cells required motile bacteria that are secretion competent. Collectively, these data suggest that the C. jejuni Cia proteins are secreted from the flagellar export apparatus.

Antigens, Bacterial↗

PubMed2004

TATA-binding protein mutants that are lethal in the absence of the Nhp6 high-mobility-group protein.

The Saccharomyces cerevisiae Nhp6 protein is related to the high-mobility-group B family of architectural DNA-binding proteins that bind DNA nonspecifically but bend DNA sharply. Nhp6 is involved in transcriptional activation by both RNA polymerase II (Pol II) and Pol III. Our previous genetic studies have implicated Nhp6 in facilitating TATA-binding protein (TBP) binding to some Pol II promoters in vivo, and we have used a novel genetic screen to isolate 32 new mutations in TBP that are viable in wild-type cells but lethal in the absence of Nhp6. The TBP mutations that are lethal in the absence of Nhp6 cluster in three regions: on the upper surface of TBP that may have a regulatory role, near residues that contact Spt3, or near residues known to contact either TFIIA or Brf1 (in TFIIIB). The latter set of mutations suggests that Nhp6 becomes essential when a TBP mutant compromises its ability to interact with either TFIIA or Brf1. Importantly, the synthetic lethality for some of the TBP mutations is suppressed by a multicopy plasmid with SNR6 or by an spt3 mutation. It has been previously shown that nhp6ab mutants are defective in expressing SNR6, a Pol III-transcribed gene encoding the U6 splicing RNA. Chromatin immunoprecipitation experiments show that TBP binding to SNR6 is reduced in an nhp6ab mutant. Nhp6 interacts with Spt16/Pob3, the yeast equivalent of the FACT elongation complex, consistent with nhp6ab cells being extremely sensitive to 6-azauracil (6-AU). However, this 6-AU sensitivity can be suppressed by multicopy SNR6 or BRF1. Additionally, strains with SNR6 promoter mutations are sensitive to 6-AU, suggesting that decreased SNR6 RNA levels contribute to 6-AU sensitivity. These results challenge the widely held belief that 6-AU sensitivity results from a defect in transcriptional elongation.

DNA-Binding Proteins↗

PubMed2004

Role for Nhp6, Gcn5, and the Swi/Snf complex in stimulating formation of the TATA-binding protein-TFIIA-DNA complex.

The TATA-binding protein (TBP), TFIIA, and TFIIB interact with promoter DNA to form a complex required for transcriptional initiation, and many transcriptional regulators function by either stimulating or inhibiting formation of this complex. We have recently identified TBP mutants that are viable in wild-type cells but lethal in the absence of the Nhp6 architectural transcription factor. Here we show that many of these TBP mutants were also lethal in strains with disruptions of either GCN5, encoding the histone acetyltransferase in the SAGA complex, or SWI2, encoding the catalytic subunit of the Swi/Snf chromatin remodeling complex. These synthetic lethalities could be suppressed by overexpression of TOA1 and TOA2, the genes encoding TFIIA. We also used TFIIA mutants that eliminated in vitro interactions with TBP. These viable TFIIA mutants were lethal in strains lacking Gcn5, Swi2, or Nhp6. These lethalities could be suppressed by overexpression of TBP or Nhp6, suggesting that these coactivators stimulate formation of the TBP-TFIIA-DNA complex. In vitro studies have previously shown that TBP binds very poorly to a TATA sequence within a nucleosome but that Swi/Snf stimulates binding of TBP and TFIIA. In vitro binding experiments presented here show that histone acetylation facilitates TBP binding to a nucleosomal binding site and that Nhp6 stimulates formation of a TBP-TFIIA-DNA complex. Consistent with the idea that Nhp6, Gcn5, and Swi/Snf have overlapping functions in vivo, nhp6a nhp6b gcn5 mutants had a severe growth defect, and mutations in both nhp6a nhp6b swi2 and gcn5 swi2 strains were lethal.

Acetylation↗

PubMed2003

Histopathological study of rabbit intestinal mucosa infected with a hybrid strain of Shigella dysenteriae 1 carrying LPS biosynthesis genes of Salmonella enterica serovar typhimurium.

The rfb gene cluster and the rfc gene of Salmonella enterica were introduced earlier into an invasive Shigella dysenteriae 1 strain by triparental cross. Antiserum was raised in rabbit against lipopolysaccharide isolated from the hybrid strain. Both the hybrid and the invasive S. dysenteriae 1 strain were found to have a titer of 1:2560 while for S. enterica, it was 1:640. Ligated ileal loops were prepared in rabbit, which were inoculated with 10(8) CFU ml(-1) each of the hybrid strain, and invasive S. dysenteriae 1 strain used as positive control. Escherichia coli K12 was also used as a negative control. After 18 h, the fluid accumulation ratios were 0.2 and 1.6 for hybrid and invasive strains of S. dysenteriae 1, respectively. Rabbit intestinal mucosa infected with hybrid S. dysenteriae 1 strain showed the presence of intact villus tips and unruptured intestinal mucosa whereas total necrosis of intestinal mucosa and villi was observed in the S. dysenteriae 1-infected region.

Animals↗

PubMed2003

Measuring billiard eigenfunctions with arbitrary trajectories.

We propose a method of measuring approximate quantum eigenfunctions in polygonalized billiard geometries, based on a quasiclassical evolution operator having a (smoothened) Perron-Frobenius kernel modulated by a phase arising from quantum considerations. Using a plane wave ansatz, we show that the condition under which this is an eigenfunction of the quasiclassical operator is identical to the condition for it to be an eigenfunction of the Schrödinger equation for polygonalized billiards. Finally, we demonstrate this technique by determining the quasiclassical eigenfunctions of the polygonalized stadium billiard using arbitrary trajectories and comparing this with the exact quantum stadium eigenfunctions.

Journal Article↗

PubMed2003

Role of microfilaments and microtubules in the invasion of INT-407 cells by Campylobacter jejuni.

The internalization mechanisms triggered by Campylobacter jejuni were studied by invasion assays conducted with different inhibitors that act on the cytoskeleton structure of eukaryotic cells. The depolymerization of microfilaments by cytochalasin-D and that of microtubules by colchicines and nocodazole inhibited the uptake of C. jejuni into INT-407 cells in a dose-dependent manner. The inhibitory effect of microfilament depolymerization on C. jejuni internalization was more pronounced than that of microtubule depolymerization. By immunofluorescence microscopic observations, it was demonstrated that both microfilaments and microtubules were localized in INT-407 cells after C. jejuni infection. These data suggest that the internalization mechanism triggered by C. jejuni is associated with the combined effect of microfilaments and microtubules of host cells.

Actin Cytoskeleton↗