During transcription, RNA polymerase (RNAP) moves processively along a DNA template, creating a complementary RNA. Here we present the development of an ultra-stable optical trapping system with ångström-level resolution, which we used to monitor transcriptional elongation by single molecules of Escherichia coli RNAP. Records showed discrete steps averaging 3.7 ± 0.6 Å, a distance equivalent to the mean rise per base found in B-DNA. By combining our results with quantitative gel analysis, we conclude that RNAP advances along DNA by a single base pair per nucleotide addition to the nascent RNA. We also determined the force-velocity relationship for transcription at both saturating and subsaturating nucleotide concentrations; fits to these data returned a characteristic distance parameter equivalent to one base pair. Global fits were inconsistent with a model for movement incorporating a power stroke tightly coupled to pyrophosphate release, but consistent with a brownian ratchet model incorporating a secondary NTP binding site.Processive molecular motors tend to move in discrete steps 1 . Recent advances in singlemolecule techniques have made it possible to observe such steps directly at length scales of a few nanometres or greater. The ability to detect individual catalytic turnovers, as monitored through motor displacement, while simultaneously controlling the force, substrate concentration, temperature or other parameters, provides a means to probe the mechanisms responsible for motility. Single-molecule measurements of stepping have supplied fresh insight into the mechanisms responsible for motion in motor proteins such as myosin, kinesin, dynein and the F 1 -ATPase 2-9 . A number of processive nucleic acid-based enzymes, such as lambda exonuclease 10,11 , RecBCD helicase 12-14 and RNAP 15-19 , have also been studied successfully by single-molecule methods, but the comparatively small size of their steps has been experimentally inaccessible up to this point. Movements through a single base pair along double-stranded DNA correspond to a displacement of just ~3.4 Å (ref. 20), which is more than 20-fold smaller than the 8-nm kinesin step 4 and sevenfold smaller than the 2-3-nm resolution limit attained in most previous work 2, 3,14,19,21 . During transcription, E. coli RNAP translocates along DNA while following its helical pitch 22 , adding ribonucleoside triphosphates (NTPs) successively to the growing RNA. The basic reaction cycle consists of binding the appropriate NTP, incorporation of the associated nucleoside monophosphate into the RNA, and release of pyrophosphate. In addition to † Present address: Department of Integrative Biology, University of California, Berkeley, California 94720, USA. * These authors contributed equally to this work.Supplementary Information is linked to the online version of the paper at www.nature.com/nature. The mechanism that leads to translocation during transcriptional elongation continues to be debated 27-32 , and at least two classes of models have been proposed....

A frequent assumption in behavioural science is that most of an animal's activities can be described in terms of a small set of stereotyped motifs. Here, we introduce a method for mapping an animal's actions, relying only upon the underlying structure of postural movement data to organize and classify behaviours. Applying this method to the ground-based behaviour of the fruit fly, Drosophila melanogaster, we find that flies perform stereotyped actions roughly 50% of the time, discovering over 100 distinguishable, stereotyped behavioural states. These include multiple modes of locomotion and grooming. We use the resulting measurements as the basis for identifying subtle sex-specific behavioural differences and revealing the low-dimensional nature of animal motions.

Escherichia coli RNA polymerase (RNAP) synthesizes RNA with remarkable fidelity in vivo 1 . Its low error rate may be achieved by means of a 'proofreading' mechanism comprised of two sequential events. The first event (backtracking) involves a transcriptionally upstream motion of RNAP through several base pairs, which carries the 3′ end of the nascent RNA transcript away from the enzyme active site. The second event (endonucleolytic cleavage) occurs after a variable delay and results in the scission and release of the most recently incorporated ribonucleotides, freeing up the active site. Here, by combining ultrastable optical trapping apparatus with a novel two-bead assay to monitor transcriptional elongation with near-base-pair precision, we observed backtracking and recovery by single molecules of RNAP. Backtracking events (~5 bp) occurred infrequently at locations throughout the DNA template and were associated with pauses lasting 20 s to >30 min. Inosine triphosphate increased the frequency of backtracking pauses, whereas the accessory proteins GreA and GreB, which stimulate the cleavage of nascent RNA, decreased the duration of such pauses.Recent studies have implicated the nucleolytic activity of RNA polymerase as part of a proofreading mechanism 2-4 , similar to that found in DNA polymerases 5 . A key feature of this proofreading mechanism is a short backtracking motion of the enzyme along the DNA template (directed upstream, opposite to the normal direction of transcriptional elongation). Similar rearward movements are thought to accompany the processes of transcriptional pausing 6-8 , arrest 9,10 , and transcription-coupled DNA repair 11 . During backtracking, the transcription bubble shifts and the DNA-RNA hybrid duplex remains in register, while the 3′ end of the RNA transcript moves away from the active site, and may even protrude into the secondary channel (nucleotide entrance pore) of the enzyme 6,7,9 , blocking the arrival of ribonucleoside triphosphates (NTPs). In its backtracked state, RNAP is able to cleave off and discard the most recently added base(s) by endonucleolysis, generating a fresh 3′ end at the active site for subsequent polymerization onto the nascent RNA chain. In this fashion, short RNA segments carrying misincorporated bases can be replaced, leading to the correction of transcriptional errors (Fig. 1a). Accessory proteins have been identified that increase transcriptional fidelity by preferentially stimulating the cleavage of misincorporated nucleotides: GreA and GreB for E. coli RNA polymerase 4 and SII/TFIIS for eukaryotic RNA polymerase II 2,3 .Correspondence and requests for materials should be addressed to S.M.B. (sblock@stanford.edu).. * These authors contributed equally to this work Supplementary Information accompanies the paper on www.nature.com/nature. Competing interests statementThe authors declare that they have no competing financial interests. We studied transcription by RNAP at physiological nucleotide concentrations using a new single-molecule assay tog...

Bacterial cells possess multiple cytoskeletal proteins involved in a wide range of cellular processes. These cytoskeletal proteins are dynamic, but the driving forces and cellular functions of these dynamics remain poorly understood. Eukaryotic cytoskeletal dynamics are often driven by motor proteins, but in bacteria no motors that drive cytoskeletal motion have been identified to date. Here, we quantitatively study the dynamics of the Escherichia coli actin homolog MreB, which is essential for the maintenance of rod-like cell shape in bacteria. We find that MreB rotates around the long axis of the cell in a persistent manner. Whereas previous studies have suggested that MreB dynamics are driven by its own polymerization, we show that MreB rotation does not depend on its own polymerization but rather requires the assembly of the peptidoglycan cell wall. The cell-wall synthesis machinery thus either constitutes a novel type of extracellular motor that exerts force on cytoplasmic MreB, or is indirectly required for an as-yetunidentified motor. Biophysical simulations suggest that one function of MreB rotation is to ensure a uniform distribution of new peptidoglycan insertion sites, a necessary condition to maintain rod shape during growth. These findings both broaden the view of cytoskeletal motors and deepen our understanding of the physical basis of bacterial morphogenesis.bacterial cytoskeletal dynamics | cell-wall organization | peptidoglycan synthesis | cell growth C ytoskeletal proteins play an important role in bacterial morphogenesis (1). Of the bacterial cytoskeletal proteins, the widely conserved actin homolog MreB is particularly important for bacterial cells to elongate and maintain a rod-like shape. MreB forms polymers that are associated with the cell membrane and distributed along the length of the cell in many rod-shaped bacteria (2). These polymeric MreB structures are essential for the maintenance of rod-like cell shape, as their disruption leads to cell rounding. Although MreB is essential for proper morphogenesis, bacterial cell shape is ultimately determined by the shape of the peptidoglycan cell-wall sacculus, which in turn is controlled by the cell-wall synthesis machinery. The cell wall, which is composed of stiff glycan strands cross-linked by flexible peptide linkers, forms a load-bearing structure that can counteract the intracellular turgor pressure. Cell-wall assembly requires peptidoglycan subunits to be synthesized, polymerized into glycan strands by transglycosylase enzymes, and cross-linked into the existing cell-wall network by transpeptidase enzymes. MreB directly or indirectly associates with a number of proteins that have been implicated in cell-wall assembly, such that MreB is believed to act upstream of the cell-wall assembly machinery to direct the synthesis enzymes to the sites of cell-wall insertion.Previous studies have demonstrated that MreB structures are dynamic in Bacillus subtilis and Caulobacter crescentus (3-7). To date, no motor proteins have been shown to either ...