Proteogenomic Analysis of Bacteria and Archaea: A 46 Organism Case Study

Experimental evidence is increasingly being used to reassess the quality and accuracy of genome annotation. Proteomics data used for this purpose, called proteogenomics, can alleviate many of the problematic areas of genome annotation, e.g. short protein validation and start site assignment. We performed a proteogenomic analysis of 46 genomes spanning eight bacterial and archaeal phyla across the tree of life. These diverse datasets facilitated the development of a robust approach for proteogenomics that is functional across genomes varying in %GC, gene content, proteomic sampling depth, phylogeny, and genome size. In addition to finding evidence for 682 novel proteins, 1336 new start sites, and numerous dubious genes, we discovered sites of post-translational maturation in the form of proteolytic cleavage of 1175 signal peptides. The number of novel proteins per genome is highly variable (median 7, mean 15, stdev 20). Moreover, comparison of novel genes with the current genes did not reveal any consistent abnormalities. Thus, we conclude that proteogenomics fulfills a yet to be understood deficiency in gene prediction. With the adoption of new sequencing technologies which have higher error rates than Sanger-based methods and the advances in proteomics, proteogenomics may become even more important in the future

Identification of Widespread Adenosine Nucleotide Binding in Mycobacterium tuberculosis

SummaryComputational prediction of protein function is frequently error-prone and incomplete. In Mycobacterium tuberculosis (Mtb), ∼25% of all genes have no predicted function and are annotated as hypothetical proteins, severely limiting our understanding of Mtb pathogenicity. Here, we utilize a high-throughput quantitative activity-based protein profiling (ABPP) platform to probe, annotate, and validate ATP-binding proteins in Mtb. We experimentally validate prior in silico predictions of >240 proteins and identify 72 hypothetical proteins as ATP binders. ATP interacts with proteins with diverse and unrelated sequences, providing an expanded view of adenosine nucleotide binding in Mtb. Several hypothetical ATP binders are essential or taxonomically limited, suggesting specialized functions in mycobacterial physiology and pathogenicity

ABRF Proteome Informatics Research Group (iPRG) 2016 Study: Inferring Proteoforms from Bottom-up Proteomics Data.

This report presents the results from the 2016 Association of Biomolecular Resource Facilities Proteome Informatics Research Group (iPRG) study on proteoform inference and false discovery rate (FDR) estimation from bottom-up proteomics data. For this study, 3 replicate Q Exactive Orbitrap liquid chromatography-tandom mass spectrometry datasets were generated from each of

Red-Emitting Manganese-doped Aluminum Nitride Phosphor

We report high efficiency luminescence with a manganese-doped aluminum nitride red-emitting phosphor under 254 nm excitation, as well as its excellent lumen maintenance in fluorescent lamp conditions, making it a candidate replacement for the widely deployed europium-doped yttria red phosphor. Solid-state reaction of aluminum nitride powders with manganese metal at 1900 °C, 10 atm N2 in a reducing environment results in nitrogen deficiency, as revealed diffuse reflectance spectra. When these powders are subsequently annealed in flowing nitrogen at 1650 °C, higher nitrogen content is recovered, resulting in white powders. Silicon was added to samples as an oxygen getter to improve emission efficiency. NEXAFS spectra and DFT calculations indicate that the Mn dopant is divalent. From DFT calculations, the UV absorption band is proposed to be due to an aluminum vacancy coupled with oxygen impurity dopants, and Mn2+ is assumed to be closely associated with this site. In contrast with some previous reports, we find that the highest quantum efficiency with 254 nm excitation (Q.E. = 0.86 ± 0.14) is obtained in aluminum nitride with a low manganese doping level of 0.06 mol.%. The principal Mn2+ decay of 1.25 ms is assigned to non-interacting Mn sites, while additional components in the microsecond range appear with higher Mn doping, consistent with Mn clustering and resultant exchange coupling. Slower components are present in samples with low Mn doping, as well as strong afterglow, assigned to trapping on shallow traps followed by detrapping and subsequent trapping on Mn

Kepler-432: a red giant interacting with one of its two long period giant planets

We report the discovery of Kepler-432b, a giant planet ($M_b = 5.41^{+0.32}_{-0.18} M_{\rm Jup}, R_b = 1.145^{+0.036}_{-0.039} R_{\rm Jup}$) transiting an evolved star $(M_\star = 1.32^{+0.10}_{-0.07} M_\odot, R_\star = 4.06^{+0.12}_{-0.08} R_\odot)$ with an orbital period of $P_b = 52.501129^{+0.000067}_{-0.000053}$ days. Radial velocities (RVs) reveal that Kepler-432b orbits its parent star with an eccentricity of $e = 0.5134^{+0.0098}_{-0.0089}$, which we also measure independently with asterodensity profiling (AP; $e=0.507^{+0.039}_{-0.114}$), thereby confirming the validity of AP on this particular evolved star. The well-determined planetary properties and unusually large mass also make this planet an important benchmark for theoretical models of super-Jupiter formation. Long-term RV monitoring detected the presence of a non-transiting outer planet (Kepler-432c; $M_c \sin{i_c} = 2.43^{+0.22}_{-0.24} M_{\rm Jup}, P_c = 406.2^{+3.9}_{-2.5}$ days), and adaptive optics imaging revealed a nearby (0\farcs87), faint companion (Kepler-432B) that is a physically bound M dwarf. The host star exhibits high signal-to-noise asteroseismic oscillations, which enable precise measurements of the stellar mass, radius and age. Analysis of the rotational splitting of the oscillation modes additionally reveals the stellar spin axis to be nearly edge-on, which suggests that the stellar spin is likely well-aligned with the orbit of the transiting planet. Despite its long period, the obliquity of the 52.5-day orbit may have been shaped by star-planet interaction in a manner similar to hot Jupiter systems, and we present observational and theoretical evidence to support this scenario. Finally, as a short-period outlier among giant planets orbiting giant stars, study of Kepler-432b may help explain the distribution of massive planets orbiting giant stars interior to 1 AU.Comment: 22 pages, 19 figures, 5 tables. Accepted to ApJ on Jan 24, 2015 (submitted Nov 11, 2014). Updated with minor changes to match published versio

Measurement of the Branching Fraction for B- --> D0 K*-

We present a measurement of the branching fraction for the decay B- --> D0 K*- using a sample of approximately 86 million BBbar pairs collected by the BaBar detector from e+e- collisions near the Y(4S) resonance. The D0 is detected through its decays to K- pi+, K- pi+ pi0 and K- pi+ pi- pi+, and the K*- through its decay to K0S pi-. We measure the branching fraction to be B.F.(B- --> D0 K*-)= (6.3 +/- 0.7(stat.) +/- 0.5(syst.)) x 10^{-4}.Comment: 7 pages, 1 postscript figure, submitted to Phys. Rev. D (Rapid Communications

A Study of Time-Dependent CP-Violating Asymmetries and Flavor Oscillations in Neutral B Decays at the Upsilon(4S)

We present a measurement of time-dependent CP-violating asymmetries in neutral B meson decays collected with the BABAR detector at the PEP-II asymmetric-energy B Factory at the Stanford Linear Accelerator Center. The data sample consists of 29.7 ${\rm fb}^{-1}$ recorded at the $\Upsilon(4S)$ resonance and 3.9 ${\rm fb}^{-1}$ off-resonance. One of the neutral B mesons, which are produced in pairs at the $\Upsilon(4S)$, is fully reconstructed in the CP decay modes $J/\psi K^0_S$, $\psi(2S) K^0_S$, $\chi_{c1} K^0_S$, $J/\psi K^{*0}$ ($K^{*0}\to K^0_S\pi^0$) and $J/\psi K^0_L$, or in flavor-eigenstate modes involving $D^{(*)}\pi/\rho/a_1$ and $J/\psi K^{*0}$ ($K^{*0}\to K^+\pi^-$). The flavor of the other neutral B meson is tagged at the time of its decay, mainly with the charge of identified leptons and kaons. The proper time elapsed between the decays is determined by measuring the distance between the decay vertices. A maximum-likelihood fit to this flavor eigenstate sample finds $\Delta m_d = 0.516\pm 0.016 {\rm (stat)} \pm 0.010 {\rm (syst)} {\rm ps}^{-1}$. The value of the asymmetry amplitude $\sin2\beta$ is determined from a simultaneous maximum-likelihood fit to the time-difference distribution of the flavor-eigenstate sample and about 642 tagged $B^0$ decays in the CP-eigenstate modes. We find $\sin2\beta=0.59\pm 0.14 {\rm (stat)} \pm 0.05 {\rm (syst)}$, demonstrating that CP violation exists in the neutral B meson system. (abridged)Comment: 58 pages, 35 figures, submitted to Physical Review

Evidence for the Rare Decay B -> K*ll and Measurement of the B -> Kll Branching Fraction

We present evidence for the flavor-changing neutral current decay $B\to K^*\ell^+\ell^-$ and a measurement of the branching fraction for the related process $B\to K\ell^+\ell^-$, where $\ell^+\ell^-$ is either an $e^+e^-$ or $\mu^+\mu^-$ pair. These decays are highly suppressed in the Standard Model, and they are sensitive to contributions from new particles in the intermediate state. The data sample comprises $123\times 10^6$ $\Upsilon(4S)\to B\bar{B}$ decays collected with the Babar detector at the PEP-II $e^+e^-$ storage ring. Averaging over $K^{(*)}$ isospin and lepton flavor, we obtain the branching fractions ${\mathcal B}(B\to K\ell^+\ell^-)=(0.65^{+0.14}_{-0.13}\pm 0.04)\times 10^{-6}$ and ${\mathcal B}(B\to K^*\ell^+\ell^-)=(0.88^{+0.33}_{-0.29}\pm 0.10)\times 10^{-6}$, where the uncertainties are statistical and systematic, respectively. The significance of the $B\to K\ell^+\ell^-$ signal is over $8\sigma$, while for $B\to K^*\ell^+\ell^-$ it is $3.3\sigma$.Comment: 7 pages, 2 postscript figues, submitted to Phys. Rev. Let

Study of e+e- --> pi+ pi- pi0 process using initial state radiation with BABAR

The process e+e- --> pi+ pi- pi0 gamma has been studied at a center-of-mass energy near the Y(4S) resonance using a 89.3 fb-1 data sample collected with the BaBar detector at the PEP-II collider. From the measured 3pi mass spectrum we have obtained the products of branching fractions for the omega and phi mesons, B(omega --> e+e-)B(omega --> 3pi)=(6.70 +/- 0.06 +/- 0.27)10-5 and B(phi --> e+e-)B(phi --> 3pi)=(4.30 +/- 0.08 +/- 0.21)10-5, and evaluated the e+e- --> pi+ pi- pi0 cross section for the e+e- center-of-mass energy range 1.05 to 3.00 GeV. About 900 e+e- --> J/psi gamma --> pi+ pi- pi0 gamma events have been selected and the branching fraction B(J/psi --> pi+ pi- pi0)=(2.18 +/- 0.19)% has been measured.Comment: 21 pages, 37 postscript figues, submitted to Phys. Rev.