DNA-segment-capture model for loop extrusion by structural maintenance of chromosome (SMC) protein complexes

AbstractCells possess remarkable control of the folding and entanglement topology of long and flexible chromosomal DNA molecules. It is thought that structural maintenance of chromosome (SMC) protein complexes play a crucial role in this, by organizing long DNAs into series of loops. Experimental data suggest that SMC complexes are able to translocate on DNA, as well as pull out lengths of DNA via a ‘loop extrusion’ process. We describe a Brownian loop-capture-ratchet model for translocation and loop extrusion based on known structural, catalytic, and DNA-binding properties of the Bacillus subtilis SMC complex. Our model provides an example of a new class of molecular motor where large conformational fluctuations of the motor ‘track’—in this case DNA—are involved in the basic translocation process. Quantitative analysis of our model leads to a series of predictions for the motor properties of SMC complexes, most strikingly a strong dependence of SMC translocation velocity and step size on tension in the DNA track that it is moving along, with ‘stalling’ occuring at subpiconewton tensions. We discuss how the same mechanism might be used by structurally related SMC complexes (Escherichia coli MukBEF and eukaryote condensin, cohesin and SMC5/6) to organize genomic DNA.

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DNA-segment-capture model for loop extrusion by structural maintenance of chromosome (SMC) protein complexes

10.1101/325373 ◽

2018 ◽

Cited By ~ 7

Author(s):

John F. Marko ◽

Paolo De Los Rios ◽

Alessandro Barducci ◽

Stephan Gruber

Keyword(s):

Protein Complexes ◽

Molecular Motor ◽

Strong Dependence ◽

Extrusion Process ◽

Chromosomal Dna ◽

Step Size ◽

E Coli ◽

Pull Out ◽

Structural Maintenance Of Chromosome ◽

Brownian Loop

AbstractCells possess remarkable control of the folding and entanglement topology of long and flexible chromosomal DNA molecules. It is thought that structural maintenance of chromosome (SMC) protein complexes play a crucial role in this, by organizing long DNAs into series of loops. Experimental data suggest that SMC complexes are able to translocate on DNA, as well as pull out lengths of DNA via a “loop extrusion” process. We describe a Brownian loop-capture-ratchet model for translocation and loop extrusion based on known structural, catalytic, and DNA-binding properties of theBacillus subtilisSMC complex. Our model provides an example of a new class of molecular motor where large conformational fluctuations of the motor ‘track’ - in this case DNA - are involved in the basic translocation process. Quantitative analysis of our model leads to a series of predictions for the motor properties of SMC complexes, most strikingly a strong dependence of SMC translocation velocity and step size on tension in the DNA track that it is moving along, with “stalling” occuring at subpiconewton tensions. We discuss how the same mechanism might be used by structurally related SMC complexes (E. coliMukBEF and eukaryote condensin, cohesin and SMC5/6) to organize genomic DNA.

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AFM images of open and collapsed states of yeast condensin suggest a scrunching model for DNA loop extrusion

10.1101/2019.12.13.867358 ◽

2019 ◽

Cited By ~ 1

Author(s):

Je-Kyung Ryu ◽

Allard J. Katan ◽

Eli O. van der Sluis ◽

Thomas Wisse ◽

Ralph de Groot ◽

...

Keyword(s):

Protein Complexes ◽

Molecular Motor ◽

Neck Size ◽

Force Microscopy ◽

Double Stranded Dna ◽

Atomic Force ◽

Condensin Complex ◽

Dna Loop ◽

Structural Maintenance Of Chromosome ◽

Collapsed States

SUMMARYStructural Maintenance of Chromosome (SMC) protein complexes are the key organizers of the spatiotemporal structure of chromosomes. The condensin SMC complex, which compacts DNA during mitosis, was recently shown to be a molecular motor that extrudes large loops of DNA. The mechanism of this unique motor, which takes large steps along DNA at low ATP consumption, remains elusive however. Here, we use Atomic Force Microscopy (AFM) to visualize the structure of yeast condensin and condensin-DNA complexes. Condensin is found to exhibit mainly open ‘O’ shapes and collapsed ‘B’ shapes, and it cycles dynamically between these two states over time. Condensin binds double-stranded DNA via a HEAT subunit and, surprisingly, also via the hinge domain. On extruded DNA loops, we observe a single condensin complex at the loop stem, where the neck size of the DNA loop correlates with the width of the condensin complex. Our results suggest that condensin extrudes DNA by a fast cyclic switching of its conformation between O and B shapes, consistent with a scrunching model.

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Microstructure and Mechanical Performance of Resistance Spot Welded Martensitic Advanced High Strength Steel

Processes ◽

10.3390/pr9061021 ◽

2021 ◽

Vol 9 (6) ◽

pp. 1021

Author(s):

Yunzhao Li ◽

Huaping Tang ◽

Ruilin Lai

Keyword(s):

Mechanical Properties ◽

Failure Modes ◽

Mechanical Performance ◽

Strong Dependence ◽

High Strength ◽

Weld Nugget ◽

Resistance Spot ◽

Pull Out ◽

Cross Tension ◽

Spot Welded

Resistance spot welded 1.2 mm (t)-thick 1400 MPa martensitic steel (MS1400) samples are fabricated and their microstructure, mechanical properties are investigated thoroughly. The mechanical performance and failure modes exhibit a strong dependence on weld-nugget size. The pull-out failure mode for MS1400 steel resistance spot welds does not follow the conventional weld-nugget size recommendation criteria of 4t0.5. Significant softening was observed due to dual phase microstructure of ferrite and martensite in the inter-critical heat affected zone (HAZ) and tempered martensite (TM) structure in sub-critical HAZ. However, the upper-critical HAZ exhibits obvious higher hardness than the nugget zone (NZ). In addition, the mechanical properties show that the cross-tension strength (CTS) is about one quarter of the tension-shear strength (TSS) of MS1400 weld joints, whilst the absorbed energy of cross-tension and tension-shear are almost identical.

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Hit the brakes – a new perspective on the loop extrusion mechanism of cohesin and other SMC complexes

Journal of Cell Science ◽

10.1242/jcs.247577 ◽

2021 ◽

Vol 134 (1) ◽

pp. jcs247577

Author(s):

Avi Matityahu ◽

Itay Onn

Keyword(s):

Present Model ◽

Protein Complexes ◽

Three Dimensional ◽

Dimensional Structure ◽

Order Structure ◽

Chromatid Cohesion ◽

Topologically Associated Domains ◽

Extrusion Mechanism ◽

New Perspective ◽

Structural Maintenance Of Chromosome

ABSTRACTThe three-dimensional structure of chromatin is determined by the action of protein complexes of the structural maintenance of chromosome (SMC) family. Eukaryotic cells contain three SMC complexes, cohesin, condensin, and a complex of Smc5 and Smc6. Initially, cohesin was linked to sister chromatid cohesion, the process that ensures the fidelity of chromosome segregation in mitosis. In recent years, a second function in the organization of interphase chromatin into topologically associated domains has been determined, and loop extrusion has emerged as the leading mechanism of this process. Interestingly, fundamental mechanistic differences exist between mitotic tethering and loop extrusion. As distinct molecular switches that aim to suppress loop extrusion in different biological contexts have been identified, we hypothesize here that loop extrusion is the default biochemical activity of cohesin and that its suppression shifts cohesin into a tethering mode. With this model, we aim to provide an explanation for how loop extrusion and tethering can coexist in a single cohesin complex and also apply it to the other eukaryotic SMC complexes, describing both similarities and differences between them. Finally, we present model-derived molecular predictions that can be tested experimentally, thus offering a new perspective on the mechanisms by which SMC complexes shape the higher-order structure of chromatin.

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Genome organization via loop extrusion, insights from polymer physics models

Briefings in Functional Genomics ◽

10.1093/bfgp/elz023 ◽

2019 ◽

Vol 19 (2) ◽

pp. 119-127 ◽

Cited By ~ 4

Author(s):

Surya K Ghosh ◽

Daniel Jost

Keyword(s):

Genome Organization ◽

Extrusion Process ◽

Polymer Physics ◽

Modern Biology ◽

Precise Information ◽

Multi Scale ◽

Topologically Associated Domains ◽

Structural Maintenance Of Chromosome ◽

Smc Proteins

Abstract Understanding how genomes fold and organize is one of the main challenges in modern biology. Recent high-throughput techniques like Hi-C, in combination with cutting-edge polymer physics models, have provided access to precise information on 3D chromosome folding to decipher the mechanisms driving such multi-scale organization. In particular, structural maintenance of chromosome (SMC) proteins play an important role in the local structuration of chromatin, putatively via a loop extrusion process. Here, we review the different polymer physics models that investigate the role of SMCs in the formation of topologically associated domains (TADs) during interphase via the formation of dynamic loops. We describe the main physical ingredients, compare them and discuss their relevance against experimental observations.

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RNA polymerases as moving barriers to condensin loop extrusion

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1907009116 ◽

2019 ◽

Vol 116 (41) ◽

pp. 20489-20499 ◽

Cited By ~ 22

Author(s):

Hugo B. Brandão ◽

Payel Paul ◽

Aafke A. van den Berg ◽

David Z. Rudner ◽

Xindan Wang ◽

...

Keyword(s):

Extrusion Process ◽

Rna Polymerases ◽

Rrna Genes ◽

Bacterial Cells ◽

Chromosome Conformation ◽

Protein Coding ◽

3D Genome ◽

Sister Chromatids ◽

Structural Maintenance Of Chromosome ◽

And Function

To separate replicated sister chromatids during mitosis, eukaryotes and prokaryotes have structural maintenance of chromosome (SMC) condensin complexes that were recently shown to organize chromosomes by a process known as DNA loop extrusion. In rapidly dividing bacterial cells, the process of separating sister chromatids occurs concomitantly with ongoing transcription. How transcription interferes with the condensin loop-extrusion process is largely unexplored, but recent experiments have shown that sites of high transcription may directionally affect condensin loop extrusion. We quantitatively investigate different mechanisms of interaction between condensin and elongating RNA polymerases (RNAPs) and find that RNAPs are likely steric barriers that can push and interact with condensins. Supported by chromosome conformation capture and chromatin immunoprecipitation for cells after transcription inhibition and RNAP degradation, we argue that translocating condensins must bypass transcribing RNAPs within ∼1 to 2 s of an encounter at rRNA genes and within ∼10 s at protein-coding genes. Thus, while individual RNAPs have little effect on the progress of loop extrusion, long, highly transcribed operons can significantly impede the extrusion process. Our data and quantitative models further suggest that bacterial condensin loop extrusion occurs by 2 independent, uncoupled motor activities; the motors translocate on DNA in opposing directions and function together to enlarge chromosomal loops, each independently bypassing steric barriers in their path. Our study provides a quantitative link between transcription and 3D genome organization and proposes a mechanism of interactions between SMC complexes and elongating transcription machinery relevant from bacteria to higher eukaryotes.

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Towards Radiation Tolerant Nanostructured Ferritic Alloys

Materials Science Forum ◽

10.4028/www.scientific.net/msf.654-656.23 ◽

2010 ◽

Vol 654-656 ◽

pp. 23-28 ◽

Cited By ~ 17

Author(s):

Michael K. Miller ◽

David T. Hoelzer ◽

Kaye F. Russell

Keyword(s):

Atom Probe Tomography ◽

Isothermal Annealing ◽

Extreme Environments ◽

Atom Probe ◽

Extrusion Process ◽

Ferritic Alloys ◽

New Class ◽

Significant Difference ◽

Radiation Tolerant ◽

Yttria Powder

The high temperature and irradiation response of a new class of nanostructured ferritic alloys have been investigated by atom probe tomography. These materials are candidate materials for use in the extreme environments that will be present in the next generation of power generating systems. Atom probe tomography has revealed that the yttria powder is forced into solid solution during the mechanical alloying process andsubsequently 2-nm-diameter Ti-, Y- and O-enriched nanoclusters are formedduring the extrusion process. These nanoclusters have been shown to be remarkably stable during isothermal annealing treatments up to 0.92 of the melting temperature and during proton irradiation up to 3 displacements per atom. No significant difference in sizes, compositions and number densities of the nanoclusters was also observed between the unirradiated and proton irradiated conditions. The grain boundaries were found to have high number densities of nanoclusters as well as chromium and tungsten segregation which pin the grain boundary to minimize creep and grain growth.

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Type I Restriction Systems: Sophisticated Molecular Machines (a Legacy of Bertani and Weigle)

Microbiology and Molecular Biology Reviews ◽

10.1128/mmbr.64.2.412-434.2000 ◽

2000 ◽

Vol 64 (2) ◽

pp. 412-434 ◽

Cited By ~ 261

Author(s):

Noreen E. Murray

Keyword(s):

Genetic Manipulation ◽

Molecular Motor ◽

Restriction Enzymes ◽

Target Sequence ◽

Type I ◽

Dna Translocation ◽

Chromosomal Dna ◽

Dna Breakage ◽

Intramolecular Communication ◽

Alternative Activities

SUMMARY Restriction enzymes are well known as reagents widely used by molecular biologists for genetic manipulation and analysis, but these reagents represent only one class (type II) of a wider range of enzymes that recognize specific nucleotide sequences in DNA molecules and detect the provenance of the DNA on the basis of specific modifications to their target sequence. Type I restriction and modification (R-M) systems are complex; a single multifunctional enzyme can respond to the modification state of its target sequence with the alternative activities of modification or restriction. In the absence of DNA modification, a type I R-M enzyme behaves like a molecular motor, translocating vast stretches of DNA towards itself before eventually breaking the DNA molecule. These sophisticated enzymes are the focus of this review, which will emphasize those aspects that give insights into more general problems of molecular and microbial biology. Current molecular experiments explore target recognition, intramolecular communication, and enzyme activities, including DNA translocation. Type I R-M systems are notable for their ability to evolve new specificities, even in laboratory cultures. This observation raises the important question of how bacteria protect their chromosomes from destruction by newly acquired restriction specifities. Recent experiments demonstrate proteolytic mechanisms by which cells avoid DNA breakage by a type I R-M system whenever their chromosomal DNA acquires unmodified target sequences. Finally, the review will reflect the present impact of genomic sequences on a field that has previously derived information almost exclusively from the analysis of bacteria commonly studied in the laboratory.

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