Mechanism and specificity of bacterial two-component signaling systems

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Biology, 2010.Includes bibliographical references (p. 57-60).Bacterial two component signaling (TCS) systems are the predominant means by which bacteria sense and respond to external signals. These systems represent a large family of paralogous proteins; often hundreds of the histidine kinase (HK) and response regulator (RR) pairs that make up a TCS system can be found in a single cell. How do these systems maintain faithful signal transmission and avoid cross-talk? To understand how specificity is determined, we examined co-evolving residues between HKs and RRs, and guided by this, aimed to rewire specificity of several activities of TCS systems. Previous work in the lab has successfully rewired specificity of histidine kinases for response regulators in the phosphotransfer reaction. By mutating different subsets of these co-evolving residues, we were able to rewire specificity of RRs in the phosphotransfer reaction, and partially rewire specificity of HKs and RRs in the phosphatase reaction. Additionally, we identified residues that may dictate specificity between two domains of the histidine kinase, and found that mutating them altered the rate of autophosphorylation. These analyses will allow rational rewiring of two component systems in vivo, and permit us to examine the fitness consequences of this altered specificity, providing insight into the evolutionary pressures on TCS systems.by Emma A. Lubin.S.M

Investigating the Atmospheric Mass Loss of the Kepler-105 Planets Straddling the Radius Gap

An intriguing pattern among exoplanets is the lack of detected planets between approximately $1.5$ R$_\oplus$ and $2.0$ R$_\oplus$. One proposed explanation for this "radius gap" is the photoevaporation of planetary atmospheres, a theory that can be tested by studying individual planetary systems. Kepler-105 is an ideal system for such testing due to the ordering and sizes of its planets. Kepler-105 is a sun-like star that hosts two planets straddling the radius gap in a rare architecture with the larger planet closer to the host star ($R_b = 2.53\pm0.07$ R$_\oplus$, $P_b = 5.41$ days, $R_c = 1.44\pm0.04$ R$_\oplus$, $P_c = 7.13$ days). If photoevaporation sculpted the atmospheres of these planets, then Kepler-105b would need to be much more massive than Kepler-105c to retain its atmosphere, given its closer proximity to the host star. To test this hypothesis, we simultaneously analyzed radial velocities (RVs) and transit timing variations (TTVs) of the Kepler-105 system, measuring disparate masses of $M_b = 10.8\pm2.3$ M$_\oplus$ ($\rho_b = 0.97\pm0.22$ g cm$^{-3}$) and $M_c = 5.6\pm1.2$ M$_\oplus$ ($\rho_c = 2.64\pm0.61$ g cm$^{-3}$). Based on these masses, the difference in gas envelope content of the Kepler-105 planets could be entirely due to photoevaporation (in 76\% of scenarios), although other mechanisms like core-powered mass loss could have played a role for some planet albedos.Comment: 14 pages, 3 figures, 2 table

The TESS-Keck Survey: Science Goals and Target Selection

Space-based transit missions such as Kepler and TESS have demonstrated that planets are ubiquitous. However, the success of these missions heavily depends on ground-based radial velocity (RV) surveys, which combined with transit photometry can yield bulk densities and orbital properties. While most Kepler host stars are too faint for detailed follow-up observations, TESS is detecting planets orbiting nearby bright stars that are more amenable to RV characterization. Here we introduce the TESS-Keck Survey (TKS), an RV program using ~100 nights on Keck/HIRES to study exoplanets identified by TESS. The primary survey aims are investigating the link between stellar properties and the compositions of small planets; studying how the diversity of system architectures depends on dynamical configurations or planet multiplicity; identifying prime candidates for atmospheric studies with JWST; and understanding the role of stellar evolution in shaping planetary systems. We present a fully-automated target selection algorithm, which yielded 103 planets in 86 systems for the final TKS sample. Most TKS hosts are inactive, solar-like, main-sequence stars (4500 K < Teff < 6000 K) at a wide range of metallicities. The selected TKS sample contains 71 small planets (Rp < 4 Re), 11 systems with multiple transiting candidates, 6 sub-day period planets and 3 planets that are in or near the habitable zone of their host star. The target selection described here will facilitate the comparison of measured planet masses, densities, and eccentricities to predictions from planet population models. Our target selection software is publicly available (at https://github.com/ashleychontos/sort-a-survey) and can be adapted for any survey which requires a balance of multiple science interests within a given telescope allocation.Comment: 23 pages, 10 figures, 5 table

Systematic Dissection and Trajectory-Scanning Mutagenesis of the Molecular Interface That Ensures Specificity of Two-Component Signaling Pathways

Two-component signal transduction systems enable bacteria to sense and respond to a wide range of environmental stimuli. Sensor histidine kinases transmit signals to their cognate response regulators via phosphorylation. The faithful transmission of information through two-component pathways and the avoidance of unwanted cross-talk require exquisite specificity of histidine kinase-response regulator interactions to ensure that cells mount the appropriate response to external signals. To identify putative specificity-determining residues, we have analyzed amino acid coevolution in two-component proteins and identified a set of residues that can be used to rationally rewire a model signaling pathway, EnvZ-OmpR. To explore how a relatively small set of residues can dictate partner selectivity, we combined alanine-scanning mutagenesis with an approach we call trajectory-scanning mutagenesis, in which all mutational intermediates between the specificity residues of EnvZ and another kinase, RstB, were systematically examined for phosphotransfer specificity. The same approach was used for the response regulators OmpR and RstA. Collectively, the results begin to reveal the molecular mechanism by which a small set of amino acids enables an individual kinase to discriminate amongst a large set of highly-related response regulators and vice versa. Our results also suggest that the mutational trajectories taken by two-component signaling proteins following gene or pathway duplication may be constrained and subject to differential selective pressures. Only some trajectories allow both the maintenance of phosphotransfer and the avoidance of unwanted cross-talk

The TESS-Keck Survey. XVI. Mass Measurements for 12 Planets in Eight Systems

With JWST's successful deployment and unexpectedly high fuel reserves, measuring the masses of sub-Neptunes transiting bright, nearby stars will soon become the bottleneck for characterizing the atmospheres of small exoplanets via transmission spectroscopy. Using a carefully curated target list and more than two years' worth of APF-Levy and Keck-HIRES Doppler monitoring, the TESS-Keck Survey is working toward alleviating this pressure. Here we present mass measurements for 11 transiting planets in eight systems that are particularly suited to atmospheric follow-up with JWST. We also report the discovery and confirmation of a temperate super-Jovian-mass planet on a moderately eccentric orbit. The sample of eight host stars, which includes one subgiant, spans early-K to late-F spectral types ($T_\mathrm{eff} =$ 5200--6200 K). We homogeneously derive planet parameters using a joint photometry and radial velocity modeling framework, discuss the planets' possible bulk compositions, and comment on their prospects for atmospheric characterization.Comment: Accepted for publication in The Astronomical Journal on 2023-Jun-22. 60 pages, 17 Tables, 28 Figure

The TESS-Keck Survey. XV. Precise Properties of 108 TESS Planets and Their Host Stars

We present the stellar and planetary properties for 85 TESS Objects of Interest (TOIs) hosting 108 planet candidates which comprise the TESS-Keck Survey (TKS) sample. We combine photometry, high-resolution spectroscopy, and Gaia parallaxes to measure precise and accurate stellar properties. We then use these parameters as inputs to a lightcurve processing pipeline to recover planetary signals and homogeneously fit their transit properties. Among these transit fits, we detect significant transit-timing variations among at least three multi-planet systems (TOI-1136, TOI-1246, TOI-1339) and at least one single-planet system (TOI-1279). We also reduce the uncertainties on planet-to-star radius ratios $R_p/R_\star$ across our sample, from a median fractional uncertainty of 8.8$\%$ among the original TOI Catalog values to 3.0$\%$ among our updated results. With this improvement, we are able to recover the Radius Gap among small TKS planets and find that the topology of the Radius Gap among our sample is broadly consistent with that measured among Kepler planets. The stellar and planetary properties presented here will facilitate follow-up investigations of both individual TOIs and broader trends in planet properties, system dynamics, and the evolution of planetary systems.Comment: Accepted at The Astronomical Journal; 21 pages, 9 figure

The TESS-Keck Survey. XII. A Dense 1.8 R ⊕ Ultra-short-period Planet Possibly Clinging to a High-mean-molecular-weight Atmosphere after the First Gigayear

The extreme environments of ultra-short-period planets (USPs) make excellent laboratories to study how exoplanets obtain, lose, retain, and/or regain gaseous atmospheres. We present the confirmation and characterization of the USP TOI-1347 b, a 1.8±0.1 R⊕ planet on a 0.85 day orbit that was detected with photometry from the TESS mission. We measured radial velocities of the TOI-1347 system using Keck/HIRES and HARPS-N and found the USP to be unusually massive at 11.1±1.2 M⊕. The measured mass and radius of TOI-1347 b imply an Earth-like bulk composition. A thin H/He envelope (&gt;0.01% by mass) can be ruled out at high confidence. The system is between 1 and 1.8 Gyr old; therefore, intensive photoevaporation should have concluded. We detected a tentative phase curve variation (3σ) and a secondary eclipse (2σ) in TESS photometry, which if confirmed could indicate the presence of a high-mean-molecular-weight atmosphere. We recommend additional optical and infrared observations to confirm the presence of an atmosphere and investigate its composition

The TESS-Keck Survey. XI. Mass Measurements for Four Transiting sub-Neptunes orbiting K dwarf TOI-1246

Multi-planet systems are valuable arenas for investigating exoplanet architectures and comparing planetary siblings. TOI-1246 is one such system, with a moderately bright K dwarf (V=11.6, K=9.9) and four transiting sub-Neptunes identified by TESS with orbital periods of 4.31 d, 5.90 d, 18.66 d, and 37.92 d. We collected 130 radial velocity observations with Keck/HIRES and TNG/HARPS-N to measure planet masses. We refit the 14 sectors of TESS photometry to refine planet radii (2.97±0.06 R⊕,2.47±0.08 R⊕,3.46±0.09 R⊕, 3.72±0.16 R⊕), and confirm the four planets. We find that TOI-1246 e is substantially more massive than the three inner planets (8.1±1.1M⊕, 8.8±1.2M⊕, 5.3±1.7M⊕, 14.8±2.3M⊕). The two outer planets, TOI-1246 d and TOI-1246 e, lie near to the 2:1 resonance (Pe/Pd=2.03) and exhibit transit timing variations. TOI-1246 is one of the brightest four-planet systems, making it amenable for continued observations. It is one of only six systems with measured masses and radii for all four transiting planets. The planet densities range from 0.70±0.24 to 3.21±0.44g/cm3, implying a range of bulk and atmospheric compositions. We also report a fifth planet candidate found in the RV data with a minimum mass of 25.6 ± 3.6 M⊕. This planet candidate is exterior to TOI-1246 e with a candidate period of 93.8 d, and we discuss the implications if it is confirmed to be planetary in nature

Global characterization of the Pho regulon in Caulobacter crescentus

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, 2014.Cataloged from PDF version of thesis.Includes bibliographical references.Bacteria must sense and respond to their environment in order to survive and proliferate. Adapting to phosphate-limited conditions is particularly critical, as phosphate is a central component of many important biomolecules. Most bacteria respond to phosphate limitation through a widely conserved pathway, composed of the phosphate transport Pst system, and downstream signal transduction pathway, PhoR-PhoB, termed the Pho system. In this thesis, I use the model organism Caulobacter crescentus to characterize the response to phosphate limitation. I use ChIP-Seq on the transcriptional regulator PhoB to globally map the Pho regulon in Caulobacter in both phosphate-starved and -replete conditions. I find that the regulatory regions of over 50 genes are bound by PhoB following phosphate limitation, and I identify a consensus PhoB binding motif in Caulobacter. I then examine the function of PhoU, which is a putative negative regulator of the Pho regulon in Caulobacter and many other bacteria. I use morphological and microarray data to demonstrate that PhoU is not a negative regulator of the Pho regulon, and that it instead acts outside the PhoR-PhoB pathway. I find that the function of PhoU is tightly linked to cellular phosphate metabolism. This work offers insight into how Caulobacter responds to nutrient stress, as well as a better understanding of the connectivity and output of the phosphate limitation response pathway.by Emma A. Lubin.Ph. D

The TESS-Keck Survey. XVI. Mass Measurements for 12 Planets in Eight Systems

With JWST’s successful deployment and unexpectedly high fuel reserves, measuring the masses of sub-Neptunes transiting bright, nearby stars will soon become the bottleneck for characterizing the atmospheres of small exoplanets via transmission spectroscopy. Using a carefully curated target list and observations from more than 2 yr of APF-Levy and Keck-HIRES Doppler monitoring, the TESS-Keck Survey is working toward alleviating this pressure. Here we present mass measurements for 11 transiting planets in eight systems that are particularly suited to atmospheric follow-up with JWST. We also report the discovery and confirmation of a temperate super-Jovian-mass planet on a moderately eccentric orbit. The sample of eight host stars, which includes one subgiant, spans early-K to late-F spectral types (T eff = 5200-6200 K). We homogeneously derive planet parameters using a joint photometry and radial velocity modeling framework, discuss the planets’ possible bulk compositions, and comment on their prospects for atmospheric characterization