Biophysics; Microtubules; Mitosis; Molecular Biology; Physics; Molecular Motor Proteins; Nanotechnology; Axoneme; Biostatistics
Public Health Interests
Biostatistics; Modeling; Nanotechnology; Noise
Swartz Program in Theoretical Neurobiology
Mechanics of Motor Proteins and the Cytoskeleton The Howard lab is fascinated by the question of how small molecules like proteins, lipids and nucleotides self-assemble into cells and tissues that are thousands to millions of times larger than molecular dimensions. How do the molecules know where they are, and whether the structures that they have made are the right size and shape? By combining highly sensitive techniques to visualize and manipulate individual biological molecules, with theory and modeling, the Howard lab is trying to understand the interaction rules that allow molecules to work together to form highly organized yet dynamic cellular structures.
The Howard lab is approaching these questions in the context of the microtubule cytoskeleton. They are interested in the molecular properties of motor proteins, especially how they operate as molecular machines to drive motion and regulate the growth and shrinkage of microtubules. In addition to biochemical and single-molecule approaches, they also study a number of cellular systems include mitosis, cilia and flagella, and the neuronal cytoskeleton.Specialized Terms: Motor proteins, Cytoskeleton; Microtubule dynamics; Cell motility; Mitosis; the Axoneme; Neuronal Morphology, Optical tweezers, Single-molecule biophysics
Extensive Research Description
Motor and Cytoskeletal Systems: From molecules to cells
How do cells measure length and time? How do they count? How do they sense their shape? These are some of the most important outstanding questions in cell and developmental biology. For example, how do proliferating cells know how big they are and when to stop growing and to start dividing? How do organs, such as brain and liver, ensure that they manufacture enough cells, but not too many? How do cells control the dimensions of their organelles, such as endosomes, cilia and mitotic spindles? How do cells make certain that they have exactly two copies of each chromosome, that they have just one cilium, but that dividing cells have exactly two mitotic-spindle poles?
These are difficult questions because they address “systems-level” processes whose length-scales and time-scales differ strikingly from those of the constituent molecules—the proteins, lipids and nucleic acids—that form the molecular building blocks of cells. The goal of our research is to find molecule-level answers to these systems-level questions. Just as a radio or a computer must be understood in terms of their constituent analog or digital circuits, cell and tissue morphology must be understood in terms of underlying molecular circuits. These circuits comprise networks of interacting molecules. What kinds of computations can they perform? How do they assemble? What feedback-control mechanisms operate to control the size, shape and organization of molecular assemblies? Reaction-diffusion equations have dominated our thinking about biological patterning since the seminar work of Turing in the 1950s; however, we argue that active, mechanical processes mediated by motor proteins and the cytoskeleton, may play an even more important role in morphogenesis than purely chemical mechanisms (Howard et al. 2011).
Research Approach: Quantitative experiments to test theoretical predictions
Our research focuses on the biochemistry and biophysics of the cytoskeleton, with particular emphasis on the mechanics of microtubulesand microtubule-basedmotor proteins. On the one hand, the lab is interested in how these proteins work: i.e. how do kinesins,dyneins and microtubules act as molecular machines to convert chemical energy derived from the hydrolysis of ATP or GTP into mechanical work used to power cell motility? And, on the other hand, we are interested in the roles that microtubules and their motors play in shaping and moving cells and tissues. For example, how do the dynamic properties of microtubules drive spindle and chromosome movements in mitosis, and how does dynein drive axonemal motility? What roles do microtubules and their motors play in mechanoreception in sensory cells and in shaping neurons in the brain?
Our approach is to combine measurement and theory (Howard 2014). The challenge is that the complexity of biological systems makes quantitative measurements and their interpretation exceedingly difficult. The key to circumventing these difficulties is the use of single-molecule techniques, in whose development our lab played an important role (e.g. Howard et al. 1989). Using single-molecule optical techniques, the interactions between the individual motor and cytoskeletal molecules can be characterized in vitro and in vivo. These interactions constitute a form of mechanical signaling (Howard 2009). We then use theory, primarily from statistical physics and non-linear dynamics, to predict how the individual interactions lead to the collective behavior of ensembles of molecules. We then test these predictions with quantitative in vivo experiments on intact cells.
Microtubules are biological polymers that alternate between periods of growth and shrinkage. This process, termed dynamic instability by its discovers Mitchison and Kirshner, is crucial for microtubule length regulation, for the exploration of intracellular space, and for cellular force generation. Despite its central role in cell biology, dynamic instability is poorly understood.
We are taking several complementary approaches to understanding dynamics..
(i) We have developed assays to study microtubule dynamics using single-molecule techniques: total-internal reflection fluorescence microscopy (Brouhard et al. 2008, and see right for motors moving along a microtubule) and optical tweezers (Bormuth et al. 2009, Jannasch et al. 2013, Trushko et al. 2013).
(ii) We have used these assays to figure out how microtubule-associated proteins (MAPs) regulate microtubule dynamics. We have shown how depolymerizing kinesins target microtubule ends and couple ATP hydrolysis to microtubule shortening (Helenius et al. 2006, Varga et a. 2006, 2009, Friel and Howard 2011); we discovered that XMAP215 is a processive polymerase (Brouhard et al. 2008, Widlund et al. 2011); and we found that the end-binding protein EB1 recognizes the nucleotide state of tubulin (Zanic et al. 2009) to increase catastrophe and to synergize with XMAP215 to increase microtubule growth rates (Zanic et al. 2013). Recently, we discovered that a yeast kinesin, Kip2, is a microtubule polymerase and has the fascinating and unexpected property that the longer the microtubule the greater is the acceleration of growth (Hibbel et al. 2015)! This is a form of positive feedback. These single-molecule studies show that we are are still scratching the surface of as far as the variety of activities kinesins and other microtubule associated proteins have on the regulation of the cytoskeleton.
(iii) Most biochemical and biophysical studies on microtubules use tubulin from mammalian brain because of the protein’s abundance in this tissue. However, brain tubulin is highly heterogeneous due to many different genes as well as post-translational modifications. We are therefore using two simplified systems - budding yeast and the Chlamydomonas cilium - to study tubulin dynamics and its regulation by MAPs in order to dissect their role in controlling microtubule length.
(iii) We are using theory to gain insight into microtubule length control (Varga et al. 2009), the catastrophe switch (Gardner et al. 2011, Bowne-Anderson et al. 2013, Bowne-Anderson et al. 2015) and the collective properties of motor proteins (Leduc et al. 2012)
The motility of cilia and flagella
That the motor protein dynein drives microtubule
sliding and bending in cilia and flagella has been known since the classic experiments of Gibbons, Brokaw and Satir in the 1960s and 1970s. However, how the activity of the dyneins is coordinated to give a periodic beat remains an open. We are bringing a new constellation of techniques to the problem. In earlier work, we hypothesized that the dyneins are coordinated through a force-sensing mechanism: sliding forces provide positive feedback that switches the activity of the motors across the axis of the axoneme (the motile structure within cilia and flagella) and couples the motors along the length of the axoneme (Riedel-Kruse et al. 2007, Howard 2009). Using high-speed imaging and high-precision image analysis, we showed that our hypothesis can account very satisfactorily for the beat of mammalian sperm.
We are now using the single-celled alga Chlamydomonas Reinhardtii as a model system to study (i) the beating of isolated, reactivated axonemes, the motile structure within cilia and flagella (Sartori et al. arXiv, 2015, Geyer et al. 2016, Sartori et al. 2016), (ii) the activity of axonemal subassemblies (Mukundan et al. 2014) and individual dynein molecules purified from these axonemes (Alper et al. 2013, 2014), and (iii) the role of hydrodynamics in shaping the beat pattern (Friedrich et al. 2010) and swimming path (Geyer et al. 2013). In this way we hope to obtain a molecular understanding of one of the most elegant and enigmatic examples of cell locomotion. Oscillators are a paradigms of emergence because the system behavior obscures the contributions of the individual players. We hope to the obtain the first truly molecular and biochemical understanding of a cellular oscillator
Branching morphology of neurons
The architecture of the brain and its constituent neurons is staggeringly complex. A fundamental insight into the working of the brain was made by the Spanish anatomist Ramon y Cajal who discovered the “dynamic polarization of neurons” (Ramon y Cajal, Nobel Lecture 1906). According to this principle, neurons are polarized cells, with dendrites and axons, usually on opposite sides of the cell body, and he deduced that the flow of information is also polarized, in a way that respects cell polarity: “nervous movement [i.e. electrical activity] in these prolongations [i.e. the dendrites] is towards the cell or axon, while it is away from the cell in the axons”. By studying the morphology of individual neurons and identifying the dendrites and axons, he was able to map the flow of information through the nervous system. Thus, an insight from cell biology, i.e. cell polarity, provided the key to understanding the functional anatomy of the brain. My intuition is that the cell biological principles underlying branching morphology will likewise provide key information about signaling and information processing by neurons.
Our goal is to understand the principles underlying the branching of neurons, especially dendrites. We and others have shown that the microtubule cytoskeleton play a fundamental role, not just in “feeding” neurons, but also in building them in the first place. Using highly branched mechanoreceptors in flies as a model system, we are trying to understand the tradeoffs between intracellular transport from the cell body into the dendrites, on the one hand, and the flow of information from the dendrites back to the cell body, on the other.
We are working on several other projects in which the dynamic and structural properties of microtubules underly important cellular processes such as mitosis (Coral-Garzon et al. 2016, Reber et al. 2013, Redemann et al. 2010, Pecreaux et al. 2006, Grill et al. 2003) and mechanotransduction (Liang et al. 2014, Liang et al. 2013, Bechstedt et al. 2010, Howard and Bechstedt et al. 2004).
A force-generating machinery maintains the spindle at the cell center during mitosis.
Garzon-Coral C, Fantana H & Howard J (2016) A force-generating machinery maintains the spindle at the cell center during mitosis. Science 352, 1124–1127.
Dynamic curvature regulation accounts for the symmetric and asymmetric beats of Chlamydomonas flagella.
Sartori P, Geyer VF, Jülicher F & Howard J (2016) Dynamic curvature regulation accounts for the symmetric and asymmetric beats of Chlamydomonas flagella. eLife 5, 343-368.
Independent control of static and dynamic components of the Chlamydomonas flagellar beat.
Geyer VF, Sartori P, Jülicher F & Howard J (2016) Independent control of static and dynamic components of the Chlamydomonas flagellar beat. Current Biology 26, 1098–1103.
Kinesin Kip2 enhances microtubule growth in vitro through length-dependent feedback on polymerization and catastrophe.
Hibbel A, Bogdanova A, Mahamdeh M, Jannasch A, Storch M, Schäffer E, Liakopoulos D & Howard J (2015). Kinesin Kip2 enhances microtubule growth in vitro through length-dependent feedback on polymerization and catastrophe. eLife 4 e10542. doi: 10.7554/eLife
Quantitative cell biology: the essential role of theory.
Howard J (2014) Quantitative cell biology: the essential role of theory. Mol Biol Cell. 25:3438-3440.
A NOMPC-dependent membrane-microtubule connector is a candidate for the gating spring in fly mechanoreceptors.
Liang X, Madrid J, Gärtner R, Verbavatz JM, Schiklenk C, Wilsch-Bräuninger M, Bogdanova A, Stenger F, Voigt A, Howard J. (2013) A NOMPC-dependent membrane-microtubule connector is a candidate for the gating spring in fly mechanoreceptors. Curr Biol. 23:755-63.
Molecular crowding creates traffic jams of kinesin motors on microtubules.
Leduc, C., Padberg-Gehle, K., Varga, V., Helbing, D., Diez, S. & Howard, J. (2012) Molecular crowding creates traffic jams of kinesin motors on microtubules. Proc. Natl. Acad. Sci. U S A. 109: 6100-6105.
Full List of PubMed Publications
- Coombes C, Yamamoto A, McClellan M, Reid TA, Plooster M, Luxton GW, Alper J, Howard J, Gardner MK: Mechanism of microtubule lumen entry for the α-tubulin acetyltransferase enzyme αTAT1. Proc Natl Acad Sci U S A. 2016 Nov 15; 2016 Nov 1. PMID: 27803321
- Pécréaux J, Redemann S, Alayan Z, Mercat B, Pastezeur S, Garzon-Coral C, Hyman AA, Howard J: The Mitotic Spindle in the One-Cell C. elegans Embryo Is Positioned with High Precision and Stability. Biophys J. 2016 Oct 18. PMID: 27760363
- Sartori P, Geyer VF, Howard J, Jülicher F: Curvature regulation of the ciliary beat through axonemal twist. Phys Rev E. 2016 Oct; 2016 Oct 28. PMID: 27841522
- Xiao X, Geyer VF, Bowne-Anderson H, Howard J, Sbalzarini IF: Automatic optimal filament segmentation with sub-pixel accuracy using generalized linear models and B-spline level-sets. Med Image Anal. 2016 Aug; 2016 Apr 4. PMID: 27104582
- Garzon-Coral C, Fantana HA, Howard J: A force-generating machinery maintains the spindle at the cell center during mitosis. Science. 2016 May 27. PMID: 27230381
- Sartori P, Geyer VF, Scholich A, Jülicher F, Howard J: Dynamic curvature regulation accounts for the symmetric and asymmetric beats of Chlamydomonas flagella. Elife. 2016 May 11; 2016 May 11. PMID: 27166516
- Battle C, Broedersz CP, Fakhri N, Geyer VF, Howard J, Schmidt CF, MacKintosh FC: Broken detailed balance at mesoscopic scales in active biological systems. Science. 2016 Apr 29. PMID: 27126047
- Geyer VF, Sartori P, Friedrich BM, Jülicher F, Howard J: Independent Control of the Static and Dynamic Components of the Chlamydomonas Flagellar Beat. Curr Biol. 2016 Apr 25; 2016 Mar 31. PMID: 27040779
- Borisy G, Heald R, Howard J, Janke C, Musacchio A, Nogales E: Microtubules: 50 years on from the discovery of tubulin. Nat Rev Mol Cell Biol. 2016 Apr 22. PMID: 27103327
- Carrillo Oesterreich F, Herzel L, Straube K, Hujer K, Howard J, Neugebauer KM: Splicing of Nascent RNA Coincides with Intron Exit from RNA Polymerase II. Cell. 2016 Apr 7; 2016 Mar 24. PMID: 27020755
- Hibbel A, Bogdanova A, Mahamdeh M, Jannasch A, Storch M, Schäffer E, Liakopoulos D, Howard J: Kinesin Kip2 enhances microtubule growth in vitro through length-dependent feedback on polymerization and catastrophe. Elife. 2015 Nov 18; 2015 Nov 18. PMID: 26576948
- Liang X, Madrid J, Howard J: The microtubule-based cytoskeleton is a component of a mechanical signaling pathway in fly campaniform receptors. Biophys J. 2014 Dec 16. PMID: 25517144
- Howard J: Quantitative cell biology: the essential role of theory. Mol Biol Cell. 2014 Nov 5. PMID: 25368416
- Podolski M, Mahamdeh M, Howard J: Stu2, the budding yeast XMAP215/Dis1 homolog, promotes assembly of yeast microtubules by increasing growth rate and decreasing catastrophe frequency. J Biol Chem. 2014 Oct 10; 2014 Aug 29. PMID: 25172511
- Howard J, McIntosh JR, Odde DJ: A brief scientific biography of Prof. Alan J. Hunt. Cell Mol Bioeng. 2013 Dec. PMID: 24683426