Functional Taxonomy of Bacterial Hyperstructures

During the cell cycle of rod-shaped bacteria, two morphogenetic processes can be discriminated: length growth of the cylindrical part of the cell and cell division by formation of two new cell poles. The morphogenetic protein complex responsible for the septation during cell division (the divisome) includes class A and class B penicillin-binding proteins (PBPs). In Escherichia coli, the class B PBP3 is specific for septal peptidoglycan synthesis. It requires the putative lipid II flippase FtsW for its localization at the division site and is necessary for the midcell localization of the class A PBP1B. In this work we show direct interactions between FtsW and PBP3 in vivo and in vitro by FRET (Fö rster resonance energy transfer) and co-immunoprecipitation experiments. These proteins are able to form a discrete complex independently of the other cell-division proteins. The K2-V42 peptide of PBP3 containing the membrane-spanning sequence is a structural determinant sufficient for interaction with FtsW and for PBP3 dimerization. By using a two-hybrid assay, the class A PBP1B was shown to interact with FtsW. However, it could not be detected in the immunoprecipitated FtsW-PBP3 complex. The periplasmic loop 9/10 of FtsW appeared to be involved in the interaction with both PBP1B and PBP3. It might play an important role in the positioning of these proteins within the divisome.

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“…The divisome is a dynamic hyperstructure (Norris et al, 2007). Its assembly is mediated by multiple protein interactions.…”

Section: Discussion Ftsw and Pbp3 Form A Subcomplexmentioning

confidence: 99%

The integral membrane FtsW protein and peptidoglycan synthase PBP3 form a subcomplex in Escherichia coli

et al. 2011

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“…It has also become clear that the higherorder chromatin structure and the nuclear architecture are important for efficient repair and genome maintenance (Misteli & Soutoglou, 2009). The concept of DNA repair hyperstructures may also be true for prokaryotes (Norris et al, 2007). Visualization of DNA DSB repair in live Bacillus subtilis cells revealed that RecN protein is recruited to the break followed by RecO and RecF proteins (Kidane et al, 2004).…”

Section: Introductionmentioning

confidence: 99%

DNA compaction in the early part of the SOS response is dependent on RecN and RecA

Odsbu

Skarstad

2014

Microbiology

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The nucleoids of undamaged Escherichia coli cells have a characteristic shape and number, which is dependent on the growth medium. Upon induction of the SOS response by a low dose of UV irradiation an extensive reorganization of the nucleoids occurred. Two distinct phases were observed by fluorescence microscopy. First, the nucleoids were found to change shape and fuse into compact structures at midcell. The compaction of the nucleoids lasted for 10-20 min and was followed by a phase where the DNA was dispersed throughout the cells. This second phase lasted for~1 h. The compaction was found to be dependent on the recombination proteins RecA, RecO and RecR as well as the SOS-inducible, SMC (structural maintenance of chromosomes)-like protein RecN. RecN protein is produced in high amounts during the first part of the SOS response. It is possible that the RecN-mediated 'compact DNA' stage at the beginning of the SOS response serves to stabilize damaged DNA prior to recombination and repair.

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“…Because cells in vivo are crowded with biomacromolecules, typically about a 20 to 30% volume fraction (77,78,265), the bag model has been challenged by concepts of higher-order structural elements derived from biochemical and physiological functions. For example, "metabolons" and "quinary" protein structures have been suggested to channel metabolites directly from one catalytic site to another (135,179,207,208,242), and a number of "hyperstructures" (154) have been enumerated to exemplify the concept of modular cytology (91). Such structural and functional elements are intuitively appealing because they could represent higher-order building blocks that make up a cell.…”

Section: Introductionmentioning

confidence: 99%

“…How are these complex cytological structures organized and related to the multiplexes at this coarse microscopic level? Though at this point the multiplexes are only hypothesized physicochemical entities, they may represent biochemical or physiological constructs or hyperstructures (154) at appropriate times during the cell cycle, such as the divisome or stressosome, derived from physiological behavior; other "-omes" could be found by analyses of genomewide interactomes of sys- FIG. 5.…”

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From Water and Ions to Crowded Biomacromolecules:In VivoStructuring of a Prokaryotic Cell

Spitzer¹

2011

Microbiol Mol Biol Rev

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SUMMARY The interactions and processes which structure prokaryotic cytoplasm (water, ions, metabolites, and biomacromolecules) and ensure the fidelity of the cell cycle are reviewed from a physicochemical perspective. Recent spectroscopic and biological evidence shows that water has no active structuring role in the cytoplasm, an unnecessary notion still entertained in the literature; water acts only as a normal solvent and biochemical reactant. Subcellular structuring arises from localizations and interactions of biomacromolecules and from the growth and modifications of their surfaces by catalytic reactions. Biomacromolecular crowding is a fundamental physicochemical characteristic of cells in vivo . Though some biochemical and physiological effects of crowding (excluded volume effect) have been documented, crowding assays with polyglycols, dextrans, etc., do not properly mimic the compositional variety of biomacromolecules in vivo . In vitro crowding assays are now being designed with proteins, which better reflect biomacromolecular environments in vivo , allowing for hydrophobic bonding and screened electrostatic interactions. I elaborate further the concept of complex vectorial biochemistry, where crowded biomacromolecules structure the cytosol into electrolyte pathways and nanopools that electrochemically “wire” the cell. Noncovalent attractions between biomacromolecules transiently supercrowd biomacromolecules into vectorial, semiconducting multiplexes with a high (35 to 95%)-volume fraction of biomacromolecules; consequently, reservoirs of less crowded cytosol appear in order to maintain the experimental average crowding of ∼25% volume fraction. This nonuniform crowding model allows for fast diffusion of biomacromolecules in the uncrowded cytosolic reservoirs, while the supercrowded vectorial multiplexes conserve the remarkable repeatability of the cell cycle by preventing confusing cross talk of concurrent biochemical reactions.

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Functional Taxonomy of Bacterial Hyperstructures

Cited by 81 publications

References 291 publications

The integral membrane FtsW protein and peptidoglycan synthase PBP3 form a subcomplex in Escherichia coli

The integral membrane FtsW protein and peptidoglycan synthase PBP3 form a subcomplex in Escherichia coli

DNA compaction in the early part of the SOS response is dependent on RecN and RecA

From Water and Ions to Crowded Biomacromolecules:In VivoStructuring of a Prokaryotic Cell

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