Replication of chromosomal DNA in eukaryotes has two major stages. Starting in the G1 phase of the cell cycle, double hexamers consisting of two copies of the Mcm2-7 replicative helicase are assembled at replication origins. Later, in S phase, the two helicases are incorporated into two oppositely oriented CMG (Cdc45-Mcm2-7-GINS) complexes that each then form the core of a replisome. Control of this “activation” step, which is triggered by the protein kinases DDK and S-CDK, is essential to ensure that each part of the genome is replicated once and only once in each cell cycle.
In this paper, Steve Bell’s and Jeff Gelles’ labs used multi-wavelength single-molecule fluorescence colocation (“CoSMoS”) methods to study in vitro the molecular mechanism of the activation process. The journal’s acceptance summary notes that “The manuscript provides new and convincing evidence that a heretofore unknown intermediate state [called “CtG”] for replication start contains multiple copies of the GINS and Cdc45 proteins prior to initiation at each origin with one double hexamer of the MCM2-7 complex. The number of GINS and Cdc45 is determined by DDK phosphorylation of the MCM’s and the probability to create an active helicase (CMG) is increased with multiple numbers of the bound ancillary factors…. The single molecule studies and biochemistry are beautifully executed providing the evidence for such intermediates…. The addition of in vivo studies demonstrates that modulating the multiplicity of DDK phosphorylation (and proposed, CtG formation) has an impact on origin usage in cells.”
together with collaborators from
Kim L.D.J., et al., DDK regulates replication initiation by controlling the multiplicity of Cdc45-GINS binding to Mcm2-7.
eLife 10, e65471 (2021)
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.
Rosen, G.A., Baek, I., et al., Dynamics of RNA polymerase II and elongation factor Spt4/5 recruitment during activator-dependent transcription
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.
Shekhar S, et al., Twinfilin bypasses assembly conditions and actin filament aging to drive barbed end depolymerization.
Journal of Cell Biology 220, e202006022 (2021)
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.
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.
Harden, T.T., et al. Alternative transcription cycle for bacterial RNA polymerase.
Nature Communications 11, 450 (2020).