Category Archives: Publications

Dynamics of RNA polymerase II and elongation factor Spt4/5 recruitment during activator-dependent transcription

DNA transcription by RNA polymerase II (RNApII) is arguably the process most central to regulation of gene expression in eukaryotic organisms.  Regulated transcription requires the formation on DNA of molecular assemblies containing not only RNApII but also dozens of accessory proteins that play pivotal roles in the process.  While we know about the structures of some of these assemblies in atomic detail, quantitative understanding of the dynamics and pathways by which the assemblies interconvert and progress through this fundamental gene expression pathway is largely lacking.

In this study we report single-molecule fluorescence microscopy studies of transcription in yeast nuclear extract, for the first time visualizing and measuring the dynamics of activator-dependent recruitment of RNApII and the central elongation factor Spt4/5 to transcription complexes.  Grace Rosen (Jeff Gelles’ labortatory, Brandeis) , Inwha Baek (Steve, Buratowski’s lab, Harvard Medical School), and collaborators elucidated the kinetically significant steps in activated RNApII transcription initiation and show for the first time that Spt4/5 dynamics are tuned to the typical lifetimes of transcription elongation complexes.  In addition to these substantive results, our work represents an important methodological advance.  As the first application of the CoSMoS (co-localization single-molecule spectroscopy) technique to activated eukaryotic transcription, it demonstrates a general method for elucidating the correlated dynamic interactions of different components of the machinery with initiation and elongation transcription complexes.  The approach is likely to find further use in studies of the mechanistic features of RNApII transcription.

https://doi.org/10.1073/pnas.2011224117
Rosen, G.A., Baek, I., et al., Dynamics of RNA polymerase II and elongation factor Spt4/5 recruitment during activator-dependent transcription
PNAS 117, 32348-32357 (2020).

Twinfilin bypasses assembly conditions and actin filament aging to drive barbed end depolymerization

The dynamic assembly, remodeling, and turnover of actin networks drives cellular processes
ranging from cell motility, endocytosis, and phagocytosis to cell division, cell and tissue
morphogenesis, and neuronal pathfinding. Here, we describe a new actin regulatory activity that changes understanding of how actin networks can be turned over. In a collaborative project with Bruce Goode’s lab, postdocs Shashank Shekhar and Greg Hoeprich used microfluidics-assisted total internal reflection fluorescence (TIRF) microscopy to show that mammalian twinfilin, an evolutionary conserved ADF/cofilin-homology protein, accelerates depolymerization at newly-assembled (ADP-Pi) but not older (ADP) actin filaments, even under assembly-promoting conditions (i.e., at G-actin concentrations above the critical concentration). Our data suggest that twinfilin molecules interact processively with the barbed end of the filament as it shrinks, blocking ATP-actin subunit addition while allowing ADP-Pi subunit dissociation. These novel activities of twinfilin reveal that cells have machinery that can bypass the normal filament aging process and induce the depolymerization of barbed ends as needed. These results may explain known genetic interactions between twinfilin and cofilin, and localization of twinfilin to the tips of filopodia and stereocilia, where actin filament barbed ends are clustered.

[ensemblevideo contentid=94fc0a2d-eaad-4ccb-84ac-7ebf799ba3ec autoplay=true]

10.1083/jcb.202006022
Shekhar S, et al., Twinfilin bypasses assembly conditions and actin filament aging to drive barbed end depolymerization.
Journal of Cell Biology 220, e202006022 (2021)

Alternative transcription cycle for bacterial RNA polymerase

DNA transcription is the most important nexus of gene regulation in all living organisms.  In recent years, single-molecule experiments have given us a new window into the mechanisms of transcription and have revealed novel, previously unsuspected molecular behaviors and mechanisms.  Ph.D. student Tim Harden used multi-color single-molecule fluorescence imaging to reveal a completely new transcription cycle for bacterial RNA polymerase.  Harden and co-authors showed that an RNA polymerase molecule in vitro frequently (in >90% of transcription events) remains bound to DNA and may again initiate transcription after it has terminated the first round of transcription.  Even more unexpectedly, this “secondary initiation” is not restricted to the same RNA.  After the first round, the polymerase can scan thousands of basepairs along the DNA and can initiate at a different start site, frequently one that is oriented in the opposite direction and produces an antisense transcript.

cannonical and alternative bacterial transcription cycles

To complement the single-molecule studies in vitro, the manuscript reports new analyses of whole-transcriptome cellular RNAs revealed by the Rend-seq method that measures transcript initiation and termination frequencies across the genome with single basepair resolution.  These provide evidence that the new transcription cycle may be responsible for initiating antisense transcription at hundreds of genomic locations in the two widely divergent bacterial species examined.  The work defines a new mechanism for the regulated production of antisense RNAs, many of which are now recognized as important agents of gene-specific regulation through control of transcription, mRNA decay, and translation.  In addition, the new transcription cycle provides a mechanism through which transcription initiation can be controlled not just through feedback networks involving multiple genes, but also through production of multiple different primary transcripts consequent to a single RNA polymerase-to-DNA recruitment event.

10.1038/s41467-019-14208-9
Harden, T.T., et al. Alternative transcription cycle for bacterial RNA polymerase.
Nature Communications 11, 450 (2020).

Synergy between cyclase-associated protein and cofilin accelerates actin filament depolymerization by two orders of magnitude

From Science at Brandeis:

“All animal and plant cells contain a highly elaborate system of filamentous protein polymers called the actin cytoskeleton, a scaffold that can be rapidly transformed to alter a cell’s shape and function. A critical step in reconfiguring this scaffold is the rapid disassembly (or turnover) of the actin filaments. But how is this achieved? It has long been known that the protein Cofilin plays a central role in this process, but it has been unclear how Cofilin achieves this feat. Cofilin can sever actin filaments into smaller fragments to promote their disassembly, but whether it also catalyzes subunit dissociation from filament ends has remained uncertain and controversial. Until now, this problem has been difficult to address because of limitations in directly observing Cofilin’s biochemical effects at filament ends….”  Dr. Shashank Shekhar, working together with Dr. Johnson Chung and “jointly mentored by Bruce Goode, Jeff Gelles and Jane Kondev, use[d] microfluidics-assisted single molecule TIRF imaging to tackle the problem.

The new study shows that Cofilin and one other protein (Srv2/CAP) intimately collaborate at one end of the actin filament to accelerate subunit dissociation by over 300-fold! These are the fastest rates of actin depolymerization ever observed. Further, these results establish a new paradigm in which a protein that decorates filament sides (Cofilin) works in concert with a protein that binds to filament ends (Srv2/CAP) to produce an activity that is orders of magnitude stronger than the that of either protein alone.”

10.1038/s41467-019-13268-1
Shekhar S. et al. Synergy between cyclase-associated protein and cofilin accelerates actin filament depolymerization by two orders of magnitude.
Nature Communications 10, 5319 (2019).

A conserved Mcm4 motif is required for Mcm2-7 double-hexamer formation and origin DNA unwinding

In this project, Kankowan Champasa from Stephen Bell’s lab at MIT collaborated with other researchers from the Bell and Gelles labs to study a key process that sets the stage for replication of chromosomal DNA. They explain “licensing of eukaryotic origins of replication requires DNA loading of two copies of the Mcm2-7 replicative helicase to form a head-to-head double-hexamer, ensuring activated helicases depart the origin bidirectionally.”  The researchers identified a conserved motif in the Mcm4 helicase subunit essential for formation of productive replication complexes.  Single-molecule fluorescence energy transfer experiments show that mutations in the motif still allow the two hexamers to come into contact, but they prevent the formation of the stable double-hexamers that perform the extensive DNA unwinding needed for replication.

10.7554/eLife.45538
A conserved Mcm4 motif is required for Mcm2-7 double-hexamer formation and origin DNA unwinding.
Champasa, K., Blank, C., Friedman, L.J., Gelles, J., and Bell, S.P.
eLife (2019) 8:e40576

Conformational Cycling within the Closed State of Grp94, an Hsp90-Family Chaperone

Grp94 is a molecular chaperone that helps to fold and maintain the folded state of “client” proteins in the endoplasmic reticulum.  Acceleration of client folding is driven by conformational changes in Grp94.  However,  the sequence of conformational changes and how these changes are coupled to the cycle of ATP hydrolysis is not well understood.  Prof. Timothy Street and his lab members Bin Huang and Ming Sun, in collaboration with Larry Friedman, did single-molecule fluorescence resonance energy transfer (FRET) experiments to directly observe conformational cycling in individual Grp94 molecules.  Their studies show that ATP hydrolysis can drive repeated cycling between alternative “closed” states of Grp94, suggesting a way that enzyme might propagate structural changes to client molecules. Chemical scheme for conformational cycling of Grp94.

10.1016/j.jmb.2019.06.004
Conformational Cycling within the Closed State of Grp94, an Hsp90-Family Chaperone
Huang, B., Friedman, L.J., Gelles, J., Sun, M., and Street, T.O.
Journal of Molecular Biology 431, 3312-3323 (2019).

Delayed inhibition mechanism for secondary channel factor regulation of ribosomal RNA transcription

RNA polymerases contain a conserved “secondary channel” in which proteins that regulate transcription can bind. In Escherichia coli bacteria, the secondary channel factors (SCFs) GreB and DksA both repress initiation of ribosomal RNA synthesis, but SCF loading and repression mechanisms are unclear.  Sarah Stumper and her collaborators used fluorescence correlation spectroscopy and multi-wavelength single-molecule fluorescence colocalization microscopy to show that the SCFs likely repress transcription through an interesting “delayed inhibition” mechanism in which the proteins arrive at DNA already complexed to RNA polymerase and block at a later stage of transcription initiation.  The work explains factors that control the relative contributions of the two proteins to regulation and suggests a mechanism by which repression is restricted to ribosomal RNA and other promoters that form short-duration complexes with RNA polymerase.

10.7554/eLife.40576
Delayed inhibition mechanism for secondary channel factor regulation of ribosomal RNA transcription.
Stumper, S.K., Ravi, H., Friedman, L.J., Mooney, R.A., Corrêa, I.R., Gershenson, A., Landick, R., and Gelles, J.
eLife (2019) 8:e40576

Abp1 regulation of branched actin networks

Branched actin filament networks formed by the Arp2/3 complex play an essential role in force production in eukaryotic cells.  Branched networks are not static components of the cytoskeleton.  Instead the times and locations of network assembly  and disassembly are tightly controlled by regulatory proteins.  Ph.D. student Siyang Guo used single-molecule fluorescence methods to show how the Abp1 protein positively regulates branched actin networks.  Remarkably, Apb1 functions by two distinct mechanisms.  The protein stimulates the formation of networks by stabilizing the binding of Arp2/3 complex to the sides of actin filaments, a precursor to branch formation.  However after branches form bound Abp1 works differently: it protects the network from GMF, the “pruning shears” protein that chops off branches during network disassembly.  Taken as a whole, the study gives deeper insight into the multiple layers of regulation that control cytoskeleton pattern formation and dynamics.  This project is part of a long-term collaboration on cytoskeletal regulation with Bruce Goode’s lab.

10.1038/s41467-018-05260-y
Abp1 promotes Arp2/3 complex-dependent actin nucleation and stabilizes branch junctions by antagonizing GMF
Siyang Guo, Olga S. Sokolova, Johnson Chung, Shae Padrick, Jeff Gelles, Bruce L. Goode
Nature Communications (2018) 9:2895.

“Synergistic assembly of human pre-spliceosomes across introns and exons”

In human genes, protein-coding regions alternate with non-coding “introns” that must be snipped out of the RNA transcript before it is used to produce a protein. The snipping is done by the spliceosome, a complex molecular machine that must assemble anew on each intron it removes.  The spliceosome must cut out exactly the segments of the messenger molecule that require removal, no more and no less, since inaccurate intron removal can produce a messenger molecule that is non-functional or that causes disease.

Implications of synergistic U2 recruitment for the mechanism of exon and intron recognition.To help understand how multiple introns are quickly and accurately removed, postdoctoral fellow Joerg Braun developed a light microscopy method by which for the first time we can observe the coordinated processes by which human spliceosomes recognize and assemble around the segments of single messenger RNA molecules.  As the eLife digest puts it: “The experiments show that spliceosomes working on different introns in the same pre-mRNA actually help each other out. As one assembles, this helps the spliceosome that processes the neighboring intron to get built. In particular, the U1snRNPs [a spliceosome sub-assembly] processing nearby introns collaborate to promote the assembly and activity of the spliceosomes. This teamwork is likely important to guarantee that multiple introns are cut out quickly and accurately.”

10.7554/eLife.37751
Synergistic assembly of human pre-spliceosomes across introns and exons.
Joerg E. Braun, Larry J. Friedman, Jeff Gelles, and Melissa J. Moore.
eLife (2018) 7:e37751.
Resources:
New plasmids reported in this article can be obtained from Addgene.
Computer software used in this research can be obtained from GitHub.

“Mechanism and timing of Mcm2-7 ring closure during DNA replication origin licensing”

Mcm2-7 is a ring-shaped DNA helicase that plays an essential role in DNA repliction in eukaryotic cells.  Two of the helicase molecules must encircle the double-stranded DNA at a replication origin, establishing a loaded, anti-parallel double-ring complex able to start replication at the appropriate cell cycle stage.  In this study, Simina Ticau together with collaborators from Steve Bell’s lab (MIT), Jeff Gelles’ lab (Brandeis), and New England BioLabs used wild-type and mutant helicases in single-molecule colocalization (“CoSMoS”) and single-molecule fluorescence resonance energy transfer (smFRET) experiments to identify the mechanisms by which regulatory factors and nucleotide hydrolysis control ring opening and coordinate loading. This work reveals the molecular processes that serve to prevent catastrophic genome damage due to incorrect or mistimed assembly of the replicative machinery.

10.1038/nsmb.3375
Mechanism and timing of Mcm2-7 ring closure during DNA replication origin licensing
Simina Ticau, Larry J Friedman, Kanokwan Champasa, Ivan R Corrêa Jr, Jeff Gelles, Stephen P Bell
Nat. Struct. Molec. Biol. (2017) 24: 309–315.