Rapid and accurate identification of new essential genes in under-studied microorganisms will significantly improve our understanding of how a cell works and the ability to re-engineer microorganisms. However, predicting essential genes across distantly related organisms remains a challenge. Here, we present a machine learning-based integrative approach that reliably transfers essential gene annotations between distantly related bacteria. We focused on four bacterial species that have well-characterized essential genes, and tested the transferability between three pairs among them. For each pair, we trained our classifier to learn traits associated with essential genes in one organism, and applied it to make predictions in the other. The predictions were then evaluated by examining the agreements with the known essential genes in the target organism. Ten-fold cross-validation in the same organism yielded AUC scores between 0.86 and 0.93. Cross-organism predictions yielded AUC scores between 0.69 and 0.89. The transferability is likely affected by growth conditions, quality of the training data set and the evolutionary distance. We are thus the first to report that gene essentiality can be reliably predicted using features trained and tested in a distantly related organism. Our approach proves more robust and portable than existing approaches, significantly extending our ability to predict essential genes beyond orthologs.

Wall-associated protein kinases (WAKs) are a new group of receptor-like kinases (RLK) recently identified in Arabidopsis. A cDNA encoding a novel WAK was isolated from rice and was named OsWAK1 (Oryza sativa WAK). The deduced amino acid sequence of OsWAK1 showed 27.6% identity to WAK2 from Arabidopsis. OsWAK1 not only has the ability of autophosphorylation but also can phosphorylate OsRFP1, a putative transcription regulator recently identified in rice. OsRFP1 strongly interacts with the kinase domain of OsWAK1. This demonstrated that OsWAK1 is a functional protein kinase. A fusion protein of OsWAK1 with GFP was found to be localized on the cell surface. Plasmolysis experiments further revealed OsWAK1 is associated with the cell wall. Northern blotting analysis showed that infection of the rice blast fungus, Magnaporthe oryzae significantly induced the OsWAK1 transcripts, and the accumulation of OsWAK1 mRNA occurred earlier and was more abundant in rice leaves infected with an incompatible race than with a compatible race of the blast fungus. OsWAK1 was also induced after treatment by mechanical wounding, SA and MeJA, but not by ABA. These results imply that OsWAK1 is a novel gene involved in plant defense. Furthermore, six transgenic rice lines with constitutive expression of OsWAK1 became resistant to the compatible race. However, OsWAK1 expression was undetectable in leaves, stems and flowers but very weak in roots under normal growth conditions. This provides functional evidence that induction of OsWAK1 as a novel RLK plays important roles in plant disease resistance.

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The human pathogen Pseudomonas aeruginosa is capable of causing both acute and chronic infections. Differences in virulence are attributable to the mode of growth: bacteria growing planktonically cause acute infections, while bacteria growing in matrix-enclosed aggregates known as biofilms are associated with chronic, persistent infections. While the contribution of the planktonic and biofilm modes of growth to virulence is now widely accepted, little is known about the role of dispersion in virulence, the active process by which biofilm bacteria switch back to the planktonic mode of growth. Here, we demonstrate that P. aeruginosa dispersed cells display a virulence phenotype distinct from those of planktonic and biofilm cells. While the highest activity of cytotoxic and degradative enzymes capable of breaking down polymeric matrix components was detected in supernatants of planktonic cells, the enzymatic activity of dispersed cell supernatants was similar to that of biofilm supernatants. Supernatants of non-dispersing ΔbdlA biofilms were characterized by a lack of many of the degradative activities. Expression of genes contributing to the virulence of P. aeruginosa was nearly 30-fold reduced in biofilm cells relative to planktonic cells. Gene expression analysis indicated dispersed cells, while dispersing from a biofilm and returning to the single cell lifestyle, to be distinct from both biofilm and planktonic cells, with virulence transcript levels being reduced up to 150-fold compared to planktonic cells. In contrast, virulence gene transcript levels were significantly increased in non-dispersing ΔbdlA and ΔdipA biofilms compared to wild-type planktonic cells. Despite this, bdlA and dipA inactivation, resulting in an inability to disperse in vitro, correlated with reduced pathogenicity and competitiveness in cross-phylum acute virulence models. In contrast, bdlA inactivation rendered P. aeruginosa more persistent upon chronic colonization of the murine lung, overall indicating that dispersion may contribute to both acute and chronic infections.

Francisella tularensis requires iron (Fe) for growth, but the biologic sources of Fe for this organism are largely unknown. We found that Francisella sp. growing in broth culture or within human macrophages can acquire Fe from the two major host Fe-binding proteins, lactoferrin (Lf) and transferrin (Tf). Fe acquisition is a potential target for novel therapies. Gallium (Ga) is a transition metal that interferes with cellular Fe metabolism by competing with Fe for uptake/utilization. Growth of either F. tularensis live vaccine strain (LVS) or Francisella novicida was inhibited by >2 M Ga chelated to Tf or Lf, with GaLf being somewhat more potent. Francisella spp. express two Fe-containing antioxidant enzymes, catalase (KatG) and Fe cofactored superoxide dismutase (FeSOD). Growth of LVS with 10 M GaTf or GaLf led to a dramatic decrease in bacterial catalase activity and in FeSOD activity that was associated with an increased susceptibility to H 2 O 2 . Ga also protected mice from intranasal challenge with F. novicida. Whereas 100% of the F. novicida-infected mice died by day 9, 75% of the mice receiving Ga continued to survive to at least day 15. Thus, a single intranasal dose of Ga followed by daily intraperitoneal Ga at a dose tolerated by the animals resulted in prolonged survival. These data support the potential utility of Ga as a therapy for F. tularensis infection of the lung.

Conjugal transfer of Ti plasmids ofThe Ti plasmids of Agrobacterium tumefaciens are conjugal elements, mediating their own transfer from donors to bacterial recipients (7). Transfer is strongly regulated and is responsive to two environmental cues, the presence of signal molecules produced by crown gall tumors, plant neoplasias induced by the pathogenic bacteria, and signal molecules produced by the donor bacteria themselves (9, 29). The tumor-produced signals, called opines, communicate to the Ti plasmids that the environment in which the host bacterium is located is conducive to horizontal dissemination (7). The bacterial signals, called quormones, control transfer by quorum sensing, ensuring that the transfer system is not activated until the donors have reached a critical population size. The two regulatory systems are linked in a hierarchical manner, with quorum sensing being controlled by opine availability (10,25,29).Expression of the three Ti plasmid transfer (tra) operons requires the quorum-sensing transcriptional activator TraR (9, 28). TraR, in turn, requires its acyl-homoserine lactone (acyl-HSL) quormone ligand N-(3-oxo-octanoyl)-L-homoserine lactone (3-oxo-C8-HSL) (38). TraR binds the acyl-HSL, forming active homodimers that bind target promoters containing an 18-bp inverted repeat called the tra box (11,18,19,30,40). Once bound, TraR in its ligand-bound dimer form activates transcription (40), presumably by interacting with one or more components of RNA polymerase.Acyl-HSL-mediated quorum-sensing systems rely on accumulation of the quormone in the environment as an indicator of the bacterial population size. The signal is produced intracellularly (9, 15), transits out of the cell by diffusion (16) or by active efflux systems (6,26), and reenters the cell, also probably by diffusion (16). In the absence of other mitigating elements, three primary factors working in concert establish the sensitivity, and therefore the population size, that sets the quorum for a given system. In the first, the rate of synthesis of the acyl-HSL signal determines the rate at which the quormone accumulates relative to the rate of increase of the bacterial population. Second, the level of expression of the gene coding for the quormone-responsive transcription factor determines the amount of target available to the acyl-HSL. Third, the affinity of the transcription factor for its cognate acyl-HSL coupled with the intracellular concentrations of the signal and the activator determine the point at which the quormone effectively converts the transcription factor to its active form.Results from in vivo analyses suggest that TraR is extraordinarily sensitive to its cognate acyl-HSL; concentrations of

Pseudomonas aeruginosa (PA) is a common bacterial pathogen, responsible for a high incidence of nosocomial and respiratory infections. KatA is the major catalase of PA that detoxifies hydrogen peroxide (H2O2), a reactive oxygen intermediate generated during aerobic respiration. Paradoxically, PA displays elevated KatA activity under anaerobic growth conditions where the substrate of KatA, H2O2, is not produced. The aim of the present study is to elucidate the mechanism underlying this phenomenon and define the role of KatA in PA during anaerobiosis using genetic, biochemical and biophysical approaches. We demonstrated that anaerobic wild-type PAO1 cells yielded higher levels of katA transcription and expression than aerobic cells, whereas a nitrite reductase mutant ΔnirS produced ∼50% the KatA activity of PAO1, suggesting that a basal NO level was required for the increased KatA activity. We also found that transcription of the katA gene was controlled, in part, by the master anaerobic regulator, ANR. A ΔkatA mutant and a mucoid mucA22 ΔkatA bacteria demonstrated increased sensitivity to acidified nitrite (an NO generator) in anaerobic planktonic and biofilm cultures. EPR spectra of anaerobic bacteria showed that levels of dinitrosyl iron complexes (DNIC), indicators of NO stress, were increased significantly in the ΔkatA mutant, and dramatically in a ΔnorCB mutant compared to basal levels of DNIC in PAO1 and ΔnirS mutant. Expression of KatA dramatically reduced the DNIC levels in ΔnorCB mutant. We further revealed direct NO-KatA interactions in vitro using EPR, optical spectroscopy and X-ray crystallography. KatA has a 5-coordinate high spin ferric heme that binds NO without prior reduction of the heme iron (K d ∼6 μM). Collectively, we conclude that KatA is expressed to protect PA against NO generated during anaerobic respiration. We proposed that such protective effects of KatA may involve buffering of free NO when potentially toxic concentrations of NO are approached.

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