Michael T. Laub

We study the molecular mechanisms and evolution of information processing at the cellular level. A defining and essential characteristic of cells is an ability to regulate their own behavior, modulating gene expression, cellular structures, motility, or metabolic state to ensure survival and proliferation. This regulatory capacity stems in large part from the coordinated action of signal transduction pathways that process information from the environment or internal cellular state. Using bacteria as model organisms, my lab aims to (i) elucidate the detailed molecular mechanisms responsible for the remarkable information-processing capability of cells, and (ii) understand the selective pressures and mechanisms that drive the evolution of signaling pathways. Our work is rooted in a desire to develop a deeper, fundamental understanding of how cells function and evolve, but it also has important medical implications, as many signaling pathways in pathogenic bacteria are needed for virulence.

(A) Schematic of a two-component signaling pathway. (B) Structure of a histidine kinase and its cognate response regulator highlighting the coevolving residues (spacefilled) that dictate interaction specificity. (C) Graph of sequence space, with specificity residue combinations in E. coli PhoQ that are functional compared to those found in naturally occurring PhoQ orthologs.

Current projects in our lab fall into four general areas, summarized below. For more information, please see http://laublab.mit.edu and our publications on PubMed.

Two-component signal transduction pathways

All cells harbor a relatively small number of signaling protein families. Through gene duplication and divergence, organisms have dramatically expanded a limited set of signaling proteins, giving rise to large, paralogous protein families that endow cells with sophisticated information-processing capabilities. Most bacteria encode dozens to hundreds of two-component signaling systems, usually comprised of a sensor histidine kinase that can respond to an environmental change or stimulus by phosphorylating a cognate response regulator that then triggers changes in cellular physiology or gene expression. We have shown that histidine kinases harbor an intrinsic ability to distinguish their cognate substrate from all possible non-cognate partners rather than relying on auxiliary factors like scaffolds. By studying patterns of amino-acid coevolution in cognate kinase-substrate pairs, we have identified the key specificity-determining residues in histidine kinases and response regulators. This work guided the rational rewiring of two-component signaling pathways and forms the foundation for current studies in three areas. (1) Protein evolution. We are studying the mechanisms by which two-component pathways diverge after duplication to create novel signaling pathways that are insulated from existing pathways. We use a combination of genetics, biochemistry, and phylogenetic studies, including ancestral reconstructions, to gain insight into the mutational trajectories that give rise to new signaling proteins. (2) Molecular recognition. Because partner specificity relies on only a handful of residues in each protein, two-component signaling pathways are amenable to systematic investigations into molecular recognition. By building large, comprehensive mutant libraries and with deep-sequencing as a readout, we are generating maps of the sequence space that underlies the kinase-substrate interaction in two-component pathways. The results are providing insight into the relationship of protein structure, function, and evolution. (3) Synthetic biology. The ability to rationally reprogram kinase and substrate specificity in two-component pathways is enabling new efforts in the design of synthetic signaling circuits in vivo.

Toxin-antitoxin systems

Another large set of paralogous proteins in bacteria are toxin-antitoxin systems. Typically, a toxin and antitoxin are co-produced from the same operon, binding each other to form an inert complex. However, in stressful conditions, such as nutrient starvation, the toxins are liberated to suppress cell growth. The induction of toxins underlies the phenomenon of persistence, in which a sub-population of bacteria avoid being killed by antibiotics that target actively growing cells. We are studying toxin-antitoxin systems from a variety of angles including efforts to discover novel systems in bacterial genomes and to identify both their mechanisms of action and the pathways that trigger their induction. We have also studied the specificity and evolution of toxin-antitoxin systems. As with two-component signaling proteins, we used analyses of amino-acid coevolution in cognate toxin-antitoxin pairs to pinpoint the residues crucial to interaction specificity. We are using these studies to map the sequence space underlying toxin-antitoxin systems and to elucidate fundamental principles of how protein-protein interactions evolve.

Cell cycle regulation

We have a long-standing interest in the molecular mechanisms that drive cell cycle progression and the establishment of cellular asymmetry in Caulobacter crescentus. Every cell division for Caulobacter is asymmetric, producing two different daughter cells - a swarmer cell and a stalked cell - that differ morphologically and, importantly, with respect to replicative capacity. Whereas the stalked cell can immediately initiate a new round of DNA replication, the swarmer cell is delayed in a G1 state and must first differentiate into a stalked cell before initiating S phase. Caulobacter cells are easily synchronized, cell cycle progression can be tracked by monitoring a series of morphological transitions, and a complete suite of genetic tools is available. Our current work focuses on understanding the genetic circuits that control two key cell cycle regulators, the highly conserved replication initiator DnaA and an essential response regulator, CtrA, that silences replication. We are mapping the complex signaling pathways that control the activities of these two regulators. For CtrA, our focus has been on a suite of two-component signaling proteins that orchestrate when and where CtrA is phosphorylated. This work has included the identification of basic mechanisms by which protein kinases are localized and activated within bacterial cells. For DnaA, we have focused on understanding how nutrient status and proteotoxic stress impact the levels and activity of DnaA. More recently, we have begun to explore the mechanisms that connect DnaA to CtrA and thereby ensure the orderly progression of cell cycle events and production of asymmetric daughter cells. Finally, we have identified and examined two novel checkpoint systems that allow Caulobacter to halt cell cycle progression in response to DNA damage.

Chromosome structure and organization

We have recently expanded our work on Caulobacter to understanding the role of chromosome structure in DNA replication, transcription, and DNA repair. We recently implemented Hi-C, a method based on chromosome-conformation-capture technology, to generate the first high-resolution map of a bacterial chromosome in vivo. This work revealed that the Caulobacter chromosome is organized into a series of topological domains. The boundaries between domains are, in most cases, established by the action of highly expressed genes and current work aims to better define how this works. We are also using Hi-C, in combination with fluorescence microscopy, genetics, and biochemical methods, to elucidate the role of DNA-binding proteins such as SMC (structural maintenance of chromosomes protein) in compacting and organizing the genome. We have also examined chromosome organization and spatial dynamics following DNA damage, particularly double-strand breaks. Additional efforts seek to determine how chromosome organization impacts other DNA-based processes such as DNA replication, transcription, and recombination.

Badrinarayanan, A., Le, T.B., Laub, M.T. (2015) "Bacterial chromosome organization and segregation" Annual Review of Cell and Developmental Biology, in press.

Badrinayanan, A., Le, T.B., Laub, M.T. (2015) "Rapid pairing and resegregation of distant homologous loci enables double-strand break repair in bacteria" Journal of Cell Biology, 210:385-400.

Podgornaia, A.I., Laub, M.T. (2015) "Pervasive degeneracy and epistasis in a protein-protein interface" Science, 347: 673-7.

Modell, J.W., Kambara, T.K., Perchuk, B.S., Laub, M.T. (2014) "A DNA damage-induced, SOS-independent checkpoint regulates cell division in Caulobacter crescentus" PLOS Biology, 12:e1001977.

Aakre, C.D., Phung, T.N., Huang, D., Laub, M.T. (2013) "A bacterial toxin inhibits DNA replication elongation through a direct interaction with the β sliding clamp" Molecular Cell, 52, 617-28.

Le, T.B., Imakaev, M.V., Mirny, L.A. & Laub, M.T. (2013) "High-resolution mapping of the spatial organization of a bacterial chromosome" Science, 342, 731-4.

Jonas, K., Liu, J., Chien, P., Laub, M.T. (2013) "Proteotoxic stress induces a cell cycle arrest by stimulating Lon to degrade the replication initiator DnaA" Cell, 154, 623-36.

Capra, E.J., Perchuk, B.S., Skerker, J.M., Laub, M.T. (2012) "Adaptive mutations that prevent cross-talk enable the expansion of paralogous signaling protein families" Cell, 150, p. 222-32.

Capra, E.J., Laub, M.T. (2012) "The evolution of two-component signal transduction systems" Annual Review of Microbiology, 66, p. 325-47.

Modell, J.W., Hopkins, A.C., Laub, M.T. (2011) "A DNA damage checkpoint in Caulobacter crescentus inhibits cell division through a direct interaction with FtsW", Genes and Development, 25, p. 1328-43.

Tsokos, C.G., Perchuk, B.S., Laub, M.T. (2011) "A dynamic complex of signaling proteins uses polar localization to regulate cell fate asymmetry in Caulobacter crescentus", Developmental Cell, 20, p. 329-41.

Chen, Y.E., Tropini, C., Jonas K., Tsokos, C.T., Huang, K.C., Laub, M.T. (2011) "A spatial gradient of protein phosphorylation underlies replicative asymmetry in a bacterium", Proc Natl Acad Sci USA, 108, p. 1052-7.

Gora, K.G., Tsokos, C.G., Chen, Y.E., Srinivasan, B.S., Perchuk, B.S., Laub, M.T. (2010) "A cell type-specific protein-protein interaction modulates transcriptional activity of a master regulator in Caulobacter crescentus", Molecular Cell, 39, p. 455-67.

Skerker, J.M., Perchuk, B.S., Siryaporn, A., Lubin, E., Ashenberg, O., Goulian, M., Laub, M.T. (2008) “Rewiring the specificity of two-component signal transduction systems”, Cell, 133, p. 1043-54.

Laub, M.T., Goulian, M. (2007) “Specificity in two-component signal transduction systems”, Annual Review of Genetics, 41, p. 121-45.