Tryptophan Operon Diversity Reveals Evolutionary Trends among Geographically Disparate Chlamydia trachomatis Ocular and Urogenital Strains Affecting Tryptophan Repressor and Synthase Function.

The obligate intracellular pathogen Chlamydia trachomatis (Ct) is the leading cause of bacterial sexually transmitted infections and blindness globally. To date, Ct urogenital strains are considered tryptophan prototrophs, utilizing indole for tryptophan synthesis within a closed-conformation tetramer comprised of two α (TrpA)- and two ß (TrpB)-subunits. In contrast, ocular strains are auxotrophs due to mutations in TrpA, relying on host tryptophan pools for survival. It has been speculated that there is strong selective pressure for urogenital strains to maintain a functional operon. Here, we performed genetic, phylogenetic, and novel functional modeling analyses of 595 geographically diverse Ct ocular, urethral, vaginal, and rectal strains with complete operon sequences. We found that ocular and urogenital, but not lymphogranuloma venereum, TrpA-coding sequences were under positive selection. However, vaginal and urethral strains exhibited greater nucleotide diversity and a higher ratio of nonsynonymous to synonymous substitutions [Pi(a)/Pi(s)] than ocular strains, suggesting a more rapid evolution of beneficial mutations. We also identified nonsynonymous amino acid changes for an ocular isolate with a urogenital backbone in the intergenic region between TrpR and TrpB at the exact binding site for YtgR-the only known iron-dependent transcription factor in Chlamydia-indicating that selective pressure has disabled the response to fluctuating iron levels. In silico effects on protein stability, ligand-binding affinity, and tryptophan repressor (TrpR) affinity for single-stranded DNA (ssDNA) measured by calculating free energy changes (ΔΔG) between Ct reference and mutant tryptophan operon proteins were also analyzed. We found that tryptophan synthase function was likely suboptimal compared to other bacterial tryptophan prototrophs and that a diversity of urogenital strain mutations rendered the synthase nonfunctional or inefficient. The novel mutations identified here affected active sites in an orthosteric manner but also hindered α- and ß-subunit allosteric interactions from distant sites, reducing efficiency of the tryptophan synthase. Importantly, strains with mutant proteins were inclined toward energy conservation by exhibiting an altered affinity for their respective ligands compared to reference strains, indicating greater fitness. This is not surprising as l-tryptophan is one of the most energetically costly amino acids to synthesize. Mutations in the tryptophan repressor gene (trpR) among urogenital strains were similarly detrimental to function. Our findings indicate that urogenital strains are evolving more rapidly than previously recognized with mutations that impact tryptophan operon function in a manner that is energetically beneficial, providing a novel host-pathogen evolutionary mechanism for intracellular survival.IMPORTANCEChlamydia trachomatis (Ct) is a major global public health concern causing sexually transmitted and ocular infections affecting over 130 million and 260 million people, respectively. Sequelae include infertility, preterm birth, ectopic pregnancy, and blindness. Ct relies on available host tryptophan pools and/or substrates to synthesize tryptophan to survive. Urogenital strains synthesize tryptophan from indole using their intact tryptophan synthase (TS). Ocular strains contain a trpA frameshift mutation that encodes a truncated TrpA with loss of TS function. We found that TS function is likely suboptimal compared to other tryptophan prototrophs and that urogenital stains contain diverse mutations that render TS nonfunctional/inefficient, evolve more rapidly than previously recognized, and impact operon function in a manner that is energetically beneficial, providing an alternative host-pathogen evolutionary mechanism for intracellular survival. Our research has broad scientific appeal since our approach can be applied to other bacteria that may explain evolution/survival in host-pathogen interactions.

Ultraviolet surprise: Efficient soft x-ray high-harmonic generation in multiply ionized plasmas.

High-harmonic generation is a universal response of matter to strong femtosecond laser fields, coherently upconverting light to much shorter wavelengths. Optimizing the conversion of laser light into soft x-rays typically demands a trade-off between two competing factors. Because of reduced quantum diffusion of the radiating electron wave function, the emission from each species is highest when a short-wavelength ultraviolet driving laser is used. However, phase matching--the constructive addition of x-ray waves from a large number of atoms--favors longer-wavelength mid-infrared lasers. We identified a regime of high-harmonic generation driven by 40-cycle ultraviolet lasers in waveguides that can generate bright beams in the soft x-ray region of the spectrum, up to photon energies of 280 electron volts. Surprisingly, the high ultraviolet refractive indices of both neutral atoms and ions enabled effective phase matching, even in a multiply ionized plasma. We observed harmonics with very narrow linewidths, while calculations show that the x-rays emerge as nearly time-bandwidth-limited pulse trains of ~100 attoseconds.

Higher-order nonlinearity of refractive index: the case of argon.

The nonlinear coefficients, n4, of the time-dependent refractive index for argon are calculated in the non-resonant optical regime. Second-order polynomial fitting of DC-Kerr, γ((2))(-ω; ω, 0, 0), electric field induced second harmonic generation (ESHG), γ((2))(-2ω; ω, ω, 0), and static second-order hyperpolarizability, γ((2))(0; 0, 0, 0), is performed using an auxiliary electric field approach to obtain the corresponding fourth-order optical properties. A number of basis sets are investigated for the fourth-order hyperpolarizability processes at 800 nm at coupled cluster singles and doubles level of theory, starting with the t-aug-cc-pV5Z basis set and expanding that basis set by adding diffuse functions and polarization functions. Comparison shows that the results obtained with the t-aug-cc-pV5Z basis are in very good agreement with the results obtained using the q-aug-cc-pV5Z, t-aug-cc-pV6Z, and q-aug-cc-pV6Z basis sets. To calculate the nonlinear refractive index n4, an approximate formula is suggested which expresses the related degenerate six-wave mixing coefficient, γ((4))(-ω; ω, -ω, ω, -ω, ω), in terms of the DC-Kerr, γ((4))(-ω; ω, 0, 0, 0, 0), ESHG, γ((4))(-2ω; ω, ω, 0, 0, 0), and the static fourth-order hyperpolarizability coefficients. The higher-order nonlinear refractive index n4 is found to be positive over the wavelengths 300 nm-2000 nm. In the infrared spectral range, the obtained values of n4 are in qualitative agreement with the results of Kramers-Kronig-based calculations.

Controlling dissociation of alkyl phenyl ketone radical cations in the strong-field regime through hydroxyl substitution position.

The hydroxy-substituted alkyl phenyl ketones 2'-, 3'- and 4'- (ortho, meta, and para) hydroxyacetophenone were excited in the strong-field regime with wavelengths ranging from 1200-1500 nm to produce the respective radical cations. For 2'- and 3'-hydroxyacetophenone, the parent molecular ion dominated the mass spectrum, and the intensity of the fragment ions remained unchanged as a function of excitation wavelength. In contrast, 4'-hydroxyacetophenone exhibited depletion of the parent molecular ion with corresponding enhanced formation of the benzoyl fragment ion upon excitation with 1370 nm as compared with other excitation wavelengths. Density functional (DFT) calculations suggest that dissociation occurs when the acetyl group in 4'-hydroxyacetophenone radical cation twists out-of-plane with respect to the phenyl ring, enabling a one-photon transition between the ground cation state D0 and the excited cation state D2 to occur. The DFT calculations also suggest that the lack of dissociation in the wavelength-resolved strong-field excitation measurements for 2'- and 3'-hydroxyacetophenone arises because both isomers have a barrier to rotation about the carbon-carbon bond connecting the phenyl and acetyl groups. These results help elucidate the effects of substituents on the torsional motion of radical cations and illustrate the potential for controlling molecular dissociation through the addition of substituents.

Strong Field Adiabatic Ionization Prepares a Launch State for Coherent Control.

We demonstrate that excitation of acetophenone with a strong field, near-infrared femtosecond pulse (1150-1500 nm) results in adiabatic ionization, producing acetophenone radical cation in the ground electronic state. The time-resolved transients of the parent and fragment ions probed with a weak 790 nm pulse reveal an order of magnitude enhancement of the peak-to-peak amplitude oscillations, ∼ 100 fs longer coherence time, and an order of magnitude increase in the ratio of parent to fragment ions in comparison with nonadiabatic ionization with a strong field 790 nm pulse. Equation of motion coupled cluster and classical wavepacket trajectory calculations support the mechanism wherein the probe pulse excites a wavepacket on the ground surface D0 to the excited D2 surface at a delay of 325 fs, resulting in dissociation to the benzoyl ion. Direct population transfer to the D2 state within the duration of a 1370 nm pump pulse eliminates wavepacket oscillation on the D0 state.

Measurement of ionic resonances in alkyl phenyl ketone cations via infrared strong field mass spectrometry.

Strong-field excitation of alkyl phenyl ketone molecules reveals an electronic resonance at 1370 nm in the radical cations upon measuring mass spectra as a function of excitation wavelength from 1240 to 1550 nm. The ratio of the benzoyl fragment ion to parent ion signal in acetophenone increases from 1:1.5 at 1240 nm excitation to 5:1 at 1370 nm (0.9 eV), and back to 1:1 at 1450 nm. Unlike acetophenone and propiophenone, the homologous molecules acetone and ethylbenzene exhibit no wavelength-dependent fragmentation patterns over the range from 1240 to 1550 nm, supporting the hypothesis that the electronic structure of the alkyl phenyl ketone cation enables the one-photon transition. Calculations on the acetophenone and propiophenone radical cations show the existence of a bright state, D2, 0.87 and 0.88 eV, respectively, above the ground-state D0 minimum. Calculations of the potential energy surfaces of the acetophenone radical cation suggest that a D2 → D0 radiationless transition precedes dissociation on D0. Upon population transfer to the D2 surface, the wavepacket motion is directed toward a three-state conical intersection (D0/D1/D2) that facilitates the photodissociation by converting electronic to vibrational energy on the D0 surface.

Measurement of an Electronic Resonance in a Ground-State, Gas-Phase Acetophenone Cation via Strong-Field Mass Spectrometry.

A one-photon ionic resonance is measured in the strong-field regime in acetophenone by recording the mass spectra as a function of excitation wavelength from 800 to 1500 nm. The ratio of the benzoyl to parent ion signals in the mass spectrum varies significantly with excitation wavelength, where the highest ratio observed upon excitation at 1370 nm (0.90 eV) indicates the presence of a one-photon resonance. At the resonant wavelength, the ratio of the benzoyl to parent ion signals increases linearly with laser intensity over a range from 1.1 × 10(13) to 6.0 × 10(13) W cm(-2). The ratio increases by a factor of 5 at 1370 nm with increasing pulse duration from 60 to 100 fs. Calculations using the equation of motion coupled cluster method support the existence of a one-photon transition from the ground ionic to a dissociative excited ionic state (0.87 eV), where motion of the acetyl group from a planar to nonplanar structure within the pulse duration enables the otherwise forbidden transition.