| 1. |
- Chai, Qian, et al.
(författare)
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Organization of Ribosomes and Nucleoids in Escherichia coli Cells during Growth and in Quiescence
- 2014
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Ingår i: Journal of Biological Chemistry. - 0021-9258 .- 1083-351X. ; 289:16, s. 11342-11352
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Tidskriftsartikel (refereegranskat)abstract
- Background: We studied ribosome and nucleoid distribution in Escherichia coli under growth and quiescence. Results: Spatially segregated ribosomes and nucleoids show drastically altered distribution in stationary phase or when treated with drugs affecting translation, transcription, nucleoid-topology, or cytoskeleton. Ribosome inheritance in daughter cells is frequently unequal. Conclusion: Cellular growth processes modulate ribosome and nucleoid distribution. Significance: This provides insight into subcellular organization of molecular machines. We have examined the distribution of ribosomes and nucleoids in live Escherichia coli cells under conditions of growth, division, and in quiescence. In exponentially growing cells translating ribosomes are interspersed among and around the nucleoid lobes, appearing as alternative bands under a fluorescence microscope. In contrast, inactive ribosomes either in stationary phase or after treatment with translation inhibitors such as chloramphenicol, tetracycline, and streptomycin gather predominantly at the cell poles and boundaries with concomitant compaction of the nucleoid. However, under all conditions, spatial segregation of the ribosomes and the nucleoids is well maintained. In dividing cells, ribosomes accumulate on both sides of the FtsZ ring at the mid cell. However, the distribution of the ribosomes among the new daughter cells is often unequal. Both the shape of the nucleoid and the pattern of ribosome distribution are also modified when the cells are exposed to rifampicin (transcription inhibitor), nalidixic acid (gyrase inhibitor), or A22 (MreB-cytoskeleton disruptor). Thus we conclude that the intracellular organization of the ribosomes and the nucleoids in bacteria are dynamic and critically dependent on cellular growth processes (replication, transcription, and translation) as well as on the integrity of the MreB cytoskeleton.
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| 2. |
- Das, D., et al.
(författare)
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Identical RNA-protein interactions in vivo and in vitro and a scheme of folding the newly synthesized proteins by ribosomes
- 2012
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Ingår i: Journal of Biological Chemistry. - 0021-9258 .- 1083-351X. ; 287:44, s. 37508-37521
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Tidskriftsartikel (refereegranskat)abstract
- Background: Ribosomal PTC acts as a protein folding modulator in vivo and in vitro. Results: A fixed set of nucleotides in the PTC interacts to fold polypeptides in vivo and in vitro. Conclusion: Folding all proteins through interaction with the same set of nucleotides in PTC implies they have intrinsic homology. Significance: Hundreds of proteins showed an identical cumulative hydrophobicity plot for amino acids.
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| 3. |
- Kirsebom, Leif A., et al.
(författare)
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Pleiomorphism in Mycobacterium
- 2012
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Ingår i: Advances in Applied Microbiology, Vol 80. - : ELSEVIER ACADEMIC PRESS INC. - 9780123943811 ; , s. 81-112
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Bokkapitel (refereegranskat)abstract
- Morphological variants in mycobacterial cultures under different growth conditions, including aging of the culture, have been shown to include fibrous aggregates, biofilms, coccoids, and spores. Here we discuss the diversity in shape and size changes demonstrated by bacterial cells with special reference to pleiomorphism observed in Mycobacterium spp. in response to nutritional and other environmental stresses. Inherent asymmetry in cell division and compartmentalization of cell interior under different growth conditions might contribute toward the observed pleiomorphism in mycobacteria. The regulatory genes comprising the bacterial signaling pathway responsible for initiating morphogenesis are speculated upon from bioinformatic identifications of genes for known sensors, kinases, and phosphatases existing in mycobacterial genomes as well as on the basis of what is known in other bacteria.
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| 4. |
- Nitharwal, Ram G., et al.
(författare)
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DNA binding activity of Helicobacter pylori DnaB helicase : the role of the N-terminal domain in modulating DNA binding activities
- 2012
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Ingår i: The FEBS Journal. - : Wiley. - 1742-464X .- 1742-4658. ; 279:2, s. 234-250
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Tidskriftsartikel (refereegranskat)abstract
- Replicative helicases are major motor proteins essential for chromosomal DNA replication in prokaryotes. Usually hexameric in solution, their DNA binding property must have different roles at stages ranging from the loading onto a branched structure at initiation from the origin to the highly processive translocation during elongation. Here, we have analysed the DNA binding activity of Helicobacter pylori (Hp) replicative helicase, DnaB. The results indicate that while the C-terminal region is important for its DNA binding activity, the N-terminus appears to dampen the proteins affinity for DNA. The masking activity of the N-terminus does not require ATP or hexamerization of HpDnaB and can be overcome by deleting the N-terminus. It can also be neutralized by engaging the N-terminus in an interaction with a partner like the C-terminus of DnaG primase. The inhibitory effect of the N-terminus on DNA binding activity is consistent with the 3D homology model of HpDnaB. Electron microscopy of the HpDnaBssDNA complex showed that HpDnaB preferentially bound at the ends of linear ssDNA and translocated along the DNA in the presence of ATP. These results provide an insight into the stimulatory and inhibitory effects of different regions of HpDnaB on DNA binding activities that may be central to the loading and translocation functions of DnaB helicases.
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| 5. |
- Nitharwal, Ram Gopal, et al.
(författare)
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Helicobacter pylori chromosomal DNA replication : Current status and future perspectives
- 2011
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Ingår i: FEBS Letters. - : Wiley. - 0014-5793 .- 1873-3468. ; 585:1, s. 7-17
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Forskningsöversikt (refereegranskat)abstract
- Helicobacter pylori causes gastritis, gastric ulcer and gastric cancer. Though DNA replication and its control are central to bacterial proliferation, pathogenesis, virulence and/or dormancy, our knowledge of DNA synthesis in slow growing pathogenic bacteria like H. pylori is still preliminary. Here, we review the current understanding of DNA replication, replication restart and recombinational repair in H. pylori. Several differences have been identified between the H. pylori and Escherichia coli replication machineries including the absence of DnaC, the helicase loader usually conserved in gram-negative bacteria. These differences suggest different mechanisms of DNA replication at initiation and restart of stalled forks in H. pylori.
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| 6. |
- Olsson, Jan A., et al.
(författare)
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Eclipse period of R1 plasmids during downshift from elevated copy number : Nonrandom selection of copies for replication
- 2012
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Ingår i: Plasmid. - : Elsevier BV. - 0147-619X .- 1095-9890. ; 67:2, s. 191-198
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Tidskriftsartikel (refereegranskat)abstract
- The classical Meselson-Stahl density-shift method was used to study replication of pOU71, a runaway-replication derivative of plasmid R1 in Escherichia coli. The miniplasmid maintained the normal low copy number of R1 during steady growth at 30 degrees C, but as growth temperatures were raised above 34 degrees C, the copy number of the plasmid increased to higher levels, and at 42 degrees C, it replicated without control in a runaway replication mode with lethal consequences for the host. The eclipse periods (minimum time between successive replication of the same DNA) of the plasmid shortened with rising copy numbers at increasing growth temperatures (Olsson et al., 2003). In this work, eclipse periods were measured during downshifts in copy number of pOU71 after it had replicated at 39 and 42 degrees C, resulting in 7- and 50-fold higher than normal plasmid copy number per cell, respectively. Eclipse periods for plasmid replication, measured during copy number downshift, suggested that plasmid R1, normally selected randomly for replication, showed a bias such that a newly replicated DNA had a higher probability of replication compared to the bulk of the RI population. However, even the unexpected nonrandom replication followed the copy number kinetics such that every generation, the plasmids underwent the normal inherited number of replication, n, independent of the actual number of plasmid copies in a newborn cell.
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| 7. |
- Pettersson, B M Fredrik, et al.
(författare)
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Draft Genome Sequence of Saccharopolyspora rectivirgula.
- 2014
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Ingår i: Genome Announcements. - 2169-8287. ; 2:1
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Tidskriftsartikel (refereegranskat)abstract
- We have sequenced the genome of Saccharopolyspora rectivirgula, the causative agent of farmer's lung disease. The draft genome consists of 182 contigs totaling 3,977,051 bp, with a GC content of 68.9%.
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| 8. |
- Pettersson, B. M. Fredrik, et al.
(författare)
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Identification and expression of stressosomal proteins in Mycobacterium marinum under various growth and stress conditions
- 2013
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Ingår i: FEMS Microbiology Letters. - : Oxford University Press (OUP). - 0378-1097 .- 1574-6968. ; 342:2, s. 98-105
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Tidskriftsartikel (refereegranskat)abstract
- Like other bacteria, Mycobacterium spp. have developed different strategies in response to environmental changes such as nutrient limitations and other different stress situations. We have identified candidate genes (rsb genes) from Mycobacterium marinum involved in the regulation of the activity of the alternative sigma factor, sigma F. This is a homolog of the master regulator of general stress response, sigma B, and the sporulation-specific sigma factor, sigma F, in Bacillus subtilis. The organization of these genes in M.marinum and B.subtilis is similar. Transcriptome and qRT-PCR data show that these genes are indeed expressed in M.marinum and that the levels of expression vary with growth phase and exposure to stress. In particular, cold stress caused a significant rise in the expression of all identified rsb and sigF genes. We discuss these data in relation to what is currently known for other Mycobacterium spp.
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| 9. |
- Sharma, Atul, et al.
(författare)
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Intracellular Locations of Replication Proteins and the Origin of Replication during Chromosome Duplication in the Slowly Growing Human Pathogen Helicobacter pylori
- 2014
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Ingår i: Journal of Bacteriology. - 0021-9193 .- 1098-5530. ; 196:5, s. 999-1011
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Tidskriftsartikel (refereegranskat)abstract
- We followed the position of the replication complex in the pathogenic bacterium Helicobacter pylori using antibodies raised against the single-stranded DNA binding protein (HpSSB) and the replicative helicase (HpDnaB). The position of the replication origin, oriC, was also localized in growing cells by fluorescence in situ hybridization (FISH) with fluorescence-labeled DNA sequences adjacent to the origin. The replisome assembled at oriC near one of the cell poles, and the two forks moved together toward the cell center as replication progressed in the growing cell. Termination and resolution of the forks occurred near midcell, on one side of the septal membrane. The duplicated copies of oriC did not separate until late in elongation, when the daughter chromosomes segregated into bilobed nucleoids, suggesting sister chromatid cohesion at or near the oriC region. Components of the replication machinery, viz., HpDnaB and HpDnaG (DNA primase), were found associated with the cell membrane. A model for the assembly and location of the H. pylori replication machinery during chromosomal duplication is presented.
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| 10. |
- Singh, Bhupender, et al.
(författare)
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Asymmetric growth and division in Mycobacterium spp. : compensatory mechanisms for non-medial septa
- 2013
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Ingår i: Molecular Microbiology. - : Wiley. - 0950-382X .- 1365-2958. ; 88:1, s. 64-76
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Tidskriftsartikel (refereegranskat)abstract
- Mycobacterium spp., rod-shaped cells belonging to the phylum Actinomycetes, lack the Min- and Noc/Slm systems responsible for preventing the placement of division sites at the poles or over the nucleoids to ensure septal assembly at mid-cell. We show that the position for establishment of the FtsZ-ring in exponentially growing Mycobacterium marinum and Mycobacterium smegmatis cells is nearly random, and that the cells often divide non-medially, producing two unequal but viable daughters. Septal sites and cellular growth disclosed by staining with the membrane-specific dye FM4-64 and fluorescent antibiotic vancomycin (FL-Vanco), respectively, showed that many division sites were off-centre, often over the nucleoids, and that apical cell growth was frequently unequal at the two poles. DNA transfer through the division septum was detected, and translocation activity was supported by the presence of a putative mycobacterial DNA translocase (MSMEG2690) at the majority of the division sites. Time-lapse imaging of single live cells through several generations confirmed both acentric division site placement and unequal polar growth in mycobacteria. Our evidence suggests that post-septal DNA transport and unequal polar growth may compensate for the non-medial division site placement in Mycobacterium spp.
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