- Silencing cryptic specialized metabolism in Streptomyces by the nucleoid-associated protein Lsr2. [Journal Article]
- EElife 2019 Jun 19; 8
- Lsr2 is a nucleoid-associated protein conserved throughout the actinobacteria, including the antibiotic-producing Streptomyces. Streptomyces species encode paralogous Lsr2 proteins (Lsr2 and Lsr2-lik…
Lsr2 is a nucleoid-associated protein conserved throughout the actinobacteria, including the antibiotic-producing Streptomyces. Streptomyces species encode paralogous Lsr2 proteins (Lsr2 and Lsr2-like, or LsrL), and we show here that of the two, Lsr2 has greater functional significance. We found that Lsr2 binds AT-rich sequences throughout the chromosome, and broadly represses gene expression. Strikingly, specialized metabolic clusters were over-represented amongst its targets, and the cryptic nature of many of these clusters appears to stem from Lsr2-mediated repression. Manipulating Lsr2 activity in model species and uncharacterized isolates resulted in the production of new metabolites not seen in wild type strains. Our results suggest that the transcriptional silencing of biosynthetic clusters by Lsr2 may protect Streptomyces from the inappropriate expression of specialized metabolites, and provide global control over Streptomyces' arsenal of signaling and antagonistic compounds.
- Nanoscale reorganizations of histone-like nucleoid structuring proteins in escherichia coli are caused by silver nanoparticles. [Journal Article]
- NNanotechnology 2019 Jun 18
- Silver nanoparticles (AgNPs) and ions (Ag+) have recently gained broad attention due to their antimicrobial effects against bacteria and other microbes. In this work, we demonstrate the use of super-…
Silver nanoparticles (AgNPs) and ions (Ag+) have recently gained broad attention due to their antimicrobial effects against bacteria and other microbes. In this work, we demonstrate the use of super-resolution fluorescence microscopy for investigating and quantifying the antimicrobial effect of AgNPs at the molecular level. We found that subjecting Escherichia coli (E. coli) bacteria to AgNPs led to nanoscale reorganization of histone-like nucleoid structuring (H-NS) proteins, an essential nucleoid associated protein in bacteria. We observed that H-NS proteins formed denser and larger clusters at the center of the bacteria after exposure to AgNPs. We quantified the spatial reorganizations of H-NS proteins by examining the changes of various spatial parameters, including the inter-molecular distances and molecular densities. Clustering analysis based on Voronoi-tessellation were also performed to characterize the change of H-NS proteins' clustering behavior. We found that AgNP-treatment led to an increase in the fraction of H-NS proteins forming clusters. Similar effects were observed for bacteria exposed to Ag+ ions, suggesting that the release of Ag+ ions plays an important role in the toxicity of AgNPs. On the other hand, we observed that AgNPs with two surface coatings showed difference in the nanoscale reorganization of H-NS proteins, indicating that particle-specific effects also contribute to the antimicrobial activities of AgNPs. Our results suggested that H-NS proteins were significantly affected by AgNPs and Ag+ ions, which has been overlooked previously. In addition, we examined the dynamic motion of AgNPs that were attached to the surface of bacteria. We expect that the current methodology can be readily applied to broadly and quantitatively study the spatial reorganization of biological macromolecules at the scale of nanometers caused by metal nanoparticles, which are expected to shed new light on the antimicrobial mechanism of metal nanoparticles.
- Organization of DNA in Mammalian Mitochondria. [Review]
- IJInt J Mol Sci 2019 Jun 05; 20(11)
- As with all organisms that must organize and condense their DNA to fit within the limited volume of a cell or a nucleus, mammalian mitochondrial DNA (mtDNA) is packaged into nucleoprotein structures …
As with all organisms that must organize and condense their DNA to fit within the limited volume of a cell or a nucleus, mammalian mitochondrial DNA (mtDNA) is packaged into nucleoprotein structures called nucleoids. In this study, we first introduce the general modes of DNA compaction, especially the role of the nucleoid-associated proteins (NAPs) that structure the bacterial chromosome. We then present the mitochondrial nucleoid and the main factors responsible for packaging of mtDNA: ARS- (autonomously replicating sequence-) binding factor 2 protein (Abf2p) in yeast and mitochondrial transcription factor A (TFAM) in mammals. We summarize the single-molecule manipulation experiments on mtDNA compaction and visualization of mitochondrial nucleoids that have led to our current knowledge on mtDNA compaction. Lastly, we discuss the possible regulatory role of DNA packaging by TFAM in DNA transactions such as mtDNA replication and transcription.
- Position effects on promoter activity in Escherichia coli and their consequences for antibiotic-resistance determinants. [Review]
- BSBiochem Soc Trans 2019 Jun 12
- The activity of any bacterial promoter is generally supposed to be set by its base sequence and the different transcription factors that bind in the local vicinity. Here, we review recent data indica…
The activity of any bacterial promoter is generally supposed to be set by its base sequence and the different transcription factors that bind in the local vicinity. Here, we review recent data indicating that the activity of the Escherichia coli lac operon promoter also depends upon its chromosomal location. Factors that affect promoter activity include the binding of nucleoid-associated proteins to neighbouring sequences, supercoiling and the activity of neighbouring promoters. We suggest that many bacterial promoters might be susceptible to similar position-dependent effects and we review recent data showing that the expression of mobile genes encoding antibiotic-resistance determinants is also location-dependent, both when carried on a bacterial chromosome or a conjugative plasmid.
- Plasmid Localization and Partition in Enterobacteriaceae. [Journal Article]
- EPEcoSal Plus 2019; 8(2)
- Plasmids are ubiquitous in the microbial world and have been identified in almost all species of bacteria that have been examined. Their localization inside the bacterial cell has been examined for a…
Plasmids are ubiquitous in the microbial world and have been identified in almost all species of bacteria that have been examined. Their localization inside the bacterial cell has been examined for about two decades; typically, they are not randomly distributed, and their positioning depends on copy number and their mode of segregation. Low-copy-number plasmids promote their own stable inheritance in their bacterial hosts by encoding active partition systems, which ensure that copies are positioned in both halves of a dividing cell. High-copy plasmids rely on passive diffusion of some copies, but many remain clustered together in the nucleoid-free regions of the cell. Here we review plasmid localization and partition (Par) systems, with particular emphasis on plasmids from Enterobacteriaceae and on recent results describing the in vivo localization properties and molecular mechanisms of each system. Partition systems also cause plasmid incompatibility such that distinct plasmids (with different replicons) with the same Par system cannot be stably maintained in the same cells. We discuss how partition-mediated incompatibility is a consequence of the partition mechanism.
- Characterization of the pleiotropic LysR-type transcription regulator LeuO of Escherichia coli. [Journal Article]
- NANucleic Acids Res 2019 Jun 11
- LeuO is a pleiotropic LysR-type transcriptional regulator (LTTR) and co-regulator of the abundant nucleoid-associated repressor protein H-NS in Gammaproteobacteria. As other LTTRs, LeuO is a tetramer…
LeuO is a pleiotropic LysR-type transcriptional regulator (LTTR) and co-regulator of the abundant nucleoid-associated repressor protein H-NS in Gammaproteobacteria. As other LTTRs, LeuO is a tetramer that is formed by dimerization of the N-terminal DNA-binding domain (DBD) and C-terminal effector-binding domain (EBD). To characterize the Escherichia coli LeuO protein, we screened for LeuO mutants that activate the cas (CRISPR-associated/Cascade) promoter more effectively than wild-type LeuO. This yielded nine mutants carrying amino acid substitutions in the dimerization interface of the regulatory EBD, as shown by solving the EBD's crystal structure. Superimposing of the crystal structures of LeuO-EBD and LeuO-S120D-EBD suggests that the Ser120 to Asp substitution triggers a structural change that is related to effector-induced structural changes of LTTRs. Corresponding functional analyses demonstrated that LeuO-S120D has a higher DNA-binding affinity than wild-type LeuO. Further, a palindromic DNA-binding core-site and a consensus sequence were identified by DNase I footprinting with LeuO-S120D as well as with the dimeric DBD. The data suggest that LeuO-S120D mimics an effector-induced form of LeuO regulating a distinct set of target loci. In general, constitutive mutants and determining the DNA-binding specificity of the DBD-dimer are feasible approaches to characterize LTTRs of unknown function.
- RocS drives chromosome segregation and nucleoid protection in Streptococcus pneumoniae. [Journal Article]
- NMNat Microbiol 2019 Jun 10
- Chromosome segregation in bacteria is poorly understood outside some prominent model strains1-5 and even less is known about how it is coordinated with other cellular processes. This is the case for …
Chromosome segregation in bacteria is poorly understood outside some prominent model strains1-5 and even less is known about how it is coordinated with other cellular processes. This is the case for the opportunistic human pathogen Streptococcus pneumoniae (the pneumococcus)6, which lacks the Min and the nucleoid occlusion systems7, and possesses only an incomplete chromosome partitioning Par(A)BS system, in which ParA is absent8. The bacterial tyrosine kinase9 CpsD, which is required for capsule production, was previously found to interfere with chromosome segregation10. Here, we identify a protein of unknown function that interacts with CpsD and drives chromosome segregation. RocS (Regulator of Chromosome Segregation) is a membrane-bound protein that interacts with both DNA and the chromosome partitioning protein ParB to properly segregate the origin of replication region to new daughter cells. In addition, we show that RocS interacts with the cell division protein FtsZ and hinders cell division. Altogether, this work reveals that RocS is the cornerstone of a nucleoid protection system ensuring proper chromosome segregation and cell division in coordination with the biogenesis of the protective capsular layer.
- Characterisation of ParB encoded on multipartite genome in Deinococcus radiodurans and their roles in radioresistance. [Journal Article]
- MRMicrobiol Res 2019 Jun - Aug; 223-225:22-32
- The Deinococcus radiodurans multipartite genome consists of 2 chromosomes and 2 plasmids Its genome encodes 4 ParA and 4 ParB proteins on different replicons. Multiple sequence alignments of ParBs en…
The Deinococcus radiodurans multipartite genome consists of 2 chromosomes and 2 plasmids Its genome encodes 4 ParA and 4 ParB proteins on different replicons. Multiple sequence alignments of ParBs encoded on these genome elements showed that ParB of primary chromosome (ParB1) is close to chromosomal type ParB and is found to be different from ParBs encoded on chromosome II (ParB2) and megaplasmid (ParB3) elements. We observed that ParB1, ParB2 and ParB3 exist as dimer in solution and these proteins interact to self but not to its homologs in D. radiodurans, suggesting the specificity in ParBs dimerization. The parB1 deletion mutant showed slow growth under normal condition and relatively reduced resistance to γ-radiation as compared to wild type. The parB2 and parB3 mutants maintained without selection pressure showed loss of radioresistance, which was not observed when maintained with selection pressure. Nearly half of the populations of these mutants showed resistance to antibiotics marked to respective genome elements. Interestingly, all the parB mutants showed increased copy numbers of cognate genome element in cells maintained with antibiotics possibly due to arrest in genome segregation. These results suggested that ParB proteins encoded on multipartite genome system in D. radiodurans form homodimer and not heterodimer with other ParB homologs, and they independently regulate the segregation of respective genome elements. The roles of ParB1 proteins in normal as well as radiation stressed growth of this bacterium have also been ascertained.
- Mitochondrial fusion is required for regulation of mitochondrial DNA replication. [Journal Article]
- PGPLoS Genet 2019; 15(6):e1008085
- Mitochondrial dynamics is an essential physiological process controlling mitochondrial content mixing and mobility to ensure proper function and localization of mitochondria at intracellular sites of…
Mitochondrial dynamics is an essential physiological process controlling mitochondrial content mixing and mobility to ensure proper function and localization of mitochondria at intracellular sites of high-energy demand. Intriguingly, for yet unknown reasons, severe impairment of mitochondrial fusion drastically affects mtDNA copy number. To decipher the link between mitochondrial dynamics and mtDNA maintenance, we studied mouse embryonic fibroblasts (MEFs) and mouse cardiomyocytes with disruption of mitochondrial fusion. Super-resolution microscopy revealed that loss of outer mitochondrial membrane (OMM) fusion, but not inner mitochondrial membrane (IMM) fusion, leads to nucleoid clustering. Remarkably, fluorescence in situ hybridization (FISH), bromouridine labeling in MEFs and assessment of mitochondrial transcription in tissue homogenates revealed that abolished OMM fusion does not affect transcription. Furthermore, the profound mtDNA depletion in mouse hearts lacking OMM fusion is not caused by defective integrity or increased mutagenesis of mtDNA, but instead we show that mitochondrial fusion is necessary to maintain the stoichiometry of the protein components of the mtDNA replisome. OMM fusion is necessary for proliferating MEFs to recover from mtDNA depletion and for the marked increase of mtDNA copy number during postnatal heart development. Our findings thus link OMM fusion to replication and distribution of mtDNA.
New Search Next
- The bacterial cell cycle, chromosome inheritance and cell growth. [Review]
- NRNat Rev Microbiol 2019 Jun 04
- All viable bacterial cells, whether they divide symmetrically or asymmetrically, must coordinate their growth, division, cell volume and shape with the inheritance of the genome. These coordinated pr…
All viable bacterial cells, whether they divide symmetrically or asymmetrically, must coordinate their growth, division, cell volume and shape with the inheritance of the genome. These coordinated processes maintain genome integrity over generations as chromosomes are duplicated and segregated during each cell cycle, and include the organization of DNA into nucleoids, controlled and faithful DNA replication, chromosome unlinking and faithful segregation into daughter cells. In this Review, we explore the contributions of chromosome structure and nucleoid organization to cell cycle regulation, detail the cellular processes involved in the initiation of DNA replication and DNA segregation and explore how those processes are linked to cell growth and cell division. Furthermore, we address how the study of a growing number of bacterial species enables the search for common principles that underlie the coordination of chromosome inheritance with the cell cycle.