Department of Microbiology Faculty & Researcher Works

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    Epistasis Analysis of Four Genes from Anabaena sp. Strain PCC 7120 Suggests a Connection between PatA and PatS in Heterocyst Pattern Formation
    (American Society for Microbiology, 2005-12) Orozco, Christine C. ; Risser, Douglas D. ; Callahan, Sean M.
    The hetR, patA, hetN, and patS genes are part of a regulatory network that regulates the differentiation and patterning of heterocysts in the filamentous cyanobacterium Anabaena sp. strain PCC 7120. In this report, the epistatic interactions of mutant alleles of these four genes have been used to refine our understanding of their relationships to one another. The hetR gene was necessary for differentiation in genetic backgrounds that normally give rise to excessive differentiation, supporting its role as the master regulator of differentiation and indicating that HetR directly regulates factors in addition to hetR and patS genes that regulate differentiation. A functional patS gene was necessary for the delayed multiple-contiguous-heterocyst phenotype observed in hetN mutants as well as for the relative lack of intercalary heterocysts in patA mutants. Epistasis results with mutant alleles of these three genes suggested that PatA attenuates the negative effects of both PatS and HetN on differentiation and promotes differentiation independent of its antagonistic effects on PatS and HetN activity. Cooverxpression of patS and hetR in a synthetic operon indicated that patS acts at a point downstream of hetR transcription in the regulatory network controlling differentiation. A model for the regulation of differentiation that is consistent with these and previous findings is presented.
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    Mutagenesis of hetR Reveals Amino Acids Necessary for HetR Function in the Heterocystous Cyanobacterium Anabaena sp. Strain PCC 7120
    (American Society for Microbiology, 2007-01) Risser, Douglas D. ; Callahan, Sean M.
    HetR is the master regulator of heterocyst differentiation in the filamentous cyanobacterium Anabaena sp. strain PCC 7120. Genetic selection was used to identify 33 amino acid substitutions in HetR that reduced the proportion of cells undergoing heterocyst differentiation to less than 2%. Conservative substitutions in the wild-type HetR protein revealed three mutations that dramatically reduced the amount of heterocyst differentiation when the mutant allele was present in place of the wild-type allele on a replicating plasmid in a mutant lacking hetR on the chromosome. An H69Y substitution resulted in heterocyst formation among less than 0.1% of cells, and D17E and G36A substitutions resulted in a Het- phenotype, compared to heterocyst formation among approximately 25% of cells with the wild-type hetR under the same conditions. The D17E substitution prevented DNA binding activity exhibited by wild-type HetR in mobility shift assays, whereas G36A and H69Y substitutions had no affect on DNA binding. D17E, G36A, and H69Y substitutions also resulted in higher levels of the corresponding HetR protein than of the wild-type protein when each was expressed from an inducible promoter in a hetR deletion strain, suggesting an effect on HetR protein turnover. Surprisingly, C48A and S152A substitutions, which were previously reported to result in a Het- phenotype, were found to have no effect on heterocyst differentiation or patterning when the corresponding mutations were introduced into an otherwise wild-type genetic background in Anabaena sp. strain PCC 7120. The clustering of mutations that satisfied the positive selection near the amino terminus suggests an important role for this part of the protein in HetR function.
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    Analysis of LuxR Regulon Gene Expression during Quorum Sensing in Vibrio fischeri
    (American Society for Microbiology, 2007-03) Qin, Nan ; Callahan, Sean M. ; Dunlap, Paul V. ; Stevens, Ann M.
    The regulation of the lux operon (luxICDABEG) of Vibrio fischeri has been intensively studied as a model for quorum sensing in proteobacteria. Two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis previously identified several non-Lux proteins in V. fischeri MJ-100 whose expression was dependent on LuxR and 3-oxo-hexanoyl L-homoserine lactone (3-oxo-C6-HSL). To determine if the LuxR-dependent regulation of the genes encoding these proteins was due to direct transcriptional control by LuxR and 3-oxo-C6-HSL or instead was due to indirect control via an unidentified regulatory element, promoters of interest were cloned into a lacZ reporter and tested for their LuxR and 3-oxo-C6-HSL dependence in recombinant Escherichia coli. The promoters for qsrP, acfA, and ribB were found to be directly activated via LuxR-3-oxo-C6-HSL. The sites of transcription initiation were established via primer extension analysis. Based on this information and the position of the lux box-binding site near position -40, all three promoters appear to have a class II-type promoter structure. In order to more fully characterize the LuxR regulon in V. fischeri MJ-100, real-time reverse transcription-PCR was used to study the temporal expression of qsrP, acfA, and ribB during the exponential and stationary phases of growth, and electrophoretic mobility shift assays were used to compare the binding affinities of LuxR to the promoters under investigation. Taken together, the results demonstrate that regulation of the production of QsrP, RibB, and AcfA is controlled directly by LuxR at the level of transcription, thereby establishing that there is a LuxR regulon in V. fischeri MJ-100 whose genes are coordinately expressed during mid-exponential growth.
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    HetF and PatA Control Levels of HetR in Anabaena sp. Strain PCC 7120
    (American Society for Microbiology, 2008-10) Risser, Douglas D. ; Callahan, Sean M.
    Anabaena sp. strain PCC 7120 is a filamentous cyanobacterium that differentiates heterocysts in response to deprivation of combined nitrogen. A hetF deletion strain lacked heterocysts and had aberrant cell morphology. Site-directed mutagenesis of the predicted active-site histidine and cysteine residues of this putative caspasehemoglobinase fold protease abolished HetF function, supporting the hypothesis that HetF is a protease. Deletion of patA, which is necessary for the formation of most intercalary heterocysts, or hetF resulted in an increase in HetR protein, and extra copies of hetF on a plasmid functionally bypassed the deletion of patA. A hetR-gfp translational fusion expressed from an inducible promoter demonstrated that hetF-dependent downregulation of HetR levels occurs rapidly in vegetative cells, as well as developing heterocysts. “Mosaic” filaments in which only one cell of a filament had a copy of hetR or hetF indicated that hetF is required for differentiation only in cells that will become heterocysts. hetF was required for transcription from a hetRdependent transcription start point of the hetR promoter and induction of transcription from the patS promoter. The inverse correlation between the level of HetR protein and transcription from hetR-dependent promoters suggests that the transcriptional activity of HetR is regulated by HetF and PatA.
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    Genetic and cytological evidence that heterocyst patterning is regulated by inhibitor gradients that promote activator decay
    (Proceedings of the National Academy of Sciences of the United States of America, 2009-11) Risser, Douglas D. ; Callahan, Sean M.
    The formation of a pattern of differentiated cells from a group of seemingly equivalent, undifferentiated cells is a central paradigm of developmental biology. Several species of filamentous cyanobacteria differentiate nitrogen-fixing heterocysts at regular intervals along unbranched filaments to form a periodic pattern of two distinct cell types. This patterning has been used to exemplify application of the activator-inhibitor model to periodic patterns in biology. The activator-inhibitor model proposes that activators and inhibitors of differentiation diffuse from source cells to form concentration gradients that in turn mediate patterning, but direct visualization of concentration gradients of activators and inhibitors has been difficult. Here we show that the periodic pattern of heterocysts produced by cyanobacteria relies on two inhibitors of heterocyst differentiation, PatS and HetN, in a manner consistent with the predictions of the activator-inhibitor model. Concentration gradients of the activator, HetR, were observed adjacent to heterocysts, the natural source of PatS and HetN, as well as adjacent to vegetative cells that were manipulated to overexpress a gene encoding either of the inhibitors. Gradients of HetR relied on posttranslational decay of HetR. Deletion of both patS and hetN genes prevented the formation of gradients of HetR, and a derivative of the inhibitors was shown to promote decay of HetR in a concentration-dependent manner. Our results provide strong support for application of the activator-inhibitor model to heterocyst patterning and, more generally, the formation of periodic patterns in biological systems.
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    Temporal and Spatial Regulation of the Four Transcription Start Sites of hetR from Anabaena sp. Strain PCC 7120
    (American Society for Microbiology, 2009-12) Rajagopalan, Ramya ; Callahan, Sean M.
    The filamentous cyanobacterium Anabaena sp. strain PCC 7120 forms nitrogen-fixing heterocysts in a periodic pattern in response to combined-nitrogen limitation in the environment. The master regulator of heterocyst differentiation, HetR, is necessary for both pattern formation and commitment of approximately every 10th cell of a filament to differentiation into a heterocyst. In this study, the individual contributions of four transcriptional start points (tsps) in regulation of transcription of hetR were assessed, and the effects of the regulatory genes patS, hetN, and patA on transcription from the tsps were determined. The tsp located at nucleotide -271 relative to the translational start site (-271 tsp) was the most tightly regulated tsp, and fluorescence from a -271 tsp-green fluorescent protein (GFP) reporter fusion was observed initially in groups of two cells and later in single cells arranged in a spatial pattern that mimicked the pattern of heterocysts that emerged. Conversely, the fluorescence from the -184 and -728/-696 tsp-GFP reporter fusions was uniform throughout filaments. Transcription from the -271 tsp was severely downregulated in a strain in which the patA gene, which encodes a positive regulator of differentiation, was deleted, and it was not detectable in strains overexpressing the genes encoding the negative regulators of differentiation, patS and hetN. In strains lacking the -271 tsp of hetR, pattern formation, the timing of commitment to differentiation, and the number of cells that differentiated into heterocysts were affected. Taken together, these results demonstrate the role of regulation of the -271 tsp of hetR in the genetic network that governs heterocyst pattern formation and differentiation.
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    Maintenance of heterocyst patterning in a filamentous cyanobacterium
    (Taylor & Francis Group, 2010-04) Zhu, Mei ; Callahan, Sean M. ; Allen, John S.
    In the absence of sufficient combined nitrogen, some filamentous cyanobacteria differentiate nitrogenfixing heterocysts at approximately every 10th cell position. As cells between heterocysts grow and divide, this initial pattern is maintained by the differentiation of a single cell approximately midway between existing heterocysts. This paper introduces a mathematical model for the maintenance of the periodic pattern of heterocysts differentiated by Anabaena sp. strain PCC 7120 based on the current experimental knowledge of the system. The model equations describe a non-diffusing activator (HetR) and two inhibitors (PatS and HetN) that undergo diffusion in a growing one-dimensional domain. The inhibitors in this model have distinct diffusion rates and temporal expression patterns. These unique aspects of the model reflect recent experimental findings regarding the molecular interactions that regulate patterning in Anabaena. Output from the model is in good agreement with both the temporal and spatial characteristics of the pattern maintenance process observed experimentally.
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    Transcriptional Regulation of the Heterocyst Patterning Gene patA from Anabaena sp. Strain PCC 7120
    (American Society for Microbiology, 2010-07) Young-Robbins, Shirley S. ; Risser, Douglas D. ; Moran, Jennifer R. ; Haselkorn, Robert ; Callahan, Sean M.
    The filamentous cyanobacterium Anabaena sp. strain PCC 7120 forms a periodic pattern of nitrogen-fixing heterocysts when grown in the absence of combined nitrogen. PatA is necessary for proper patterning of heterocysts along filaments. In this study, apparent transcriptional start points (tsps) were identified at nucleotides -305, -614, and -645 relative to the translational start site (-305, -614, and -645 tsps). Transcriptional reporter fusions were used to show that transcription from the -305 tsp was induced in all cells of filaments in response to nitrogen deprivation, required hetR for induction, and increased in a patA mutant. Transcription from -614/-645 tsp reporter fusions was spatially regulated and occurred primarily in cells that would become heterocysts. Complementation of a patA mutant strain by alleles encoding substitutions in, or deletion of, the putative phosphoacceptor C-terminal domain indicates that the PATAN domain can function independently of the C-terminal domain of PatA. Localization of a ring of PatA-GFP at sites of cell division, as well as the formation of enlarged cells with altered cell morphology when patA was overexpressed, suggests that PatA may participate in cell division.
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    Structure of transcription factor HetR required for heterocyst differentiation in cyanobacteria
    (Proceedings of the National Academy of Sciences of the United States of America, 2011-04) Kim, Youngchang ; Joachimiak, Grazyna ; Ye, Zi ; Binkowski, T. Andrew ; Zhang, Rongguang ; Gornicki, Piotr ; Callahan, Sean M. ; Hess, Wolfgang R. ; Haselkorn, Robert ; Joachimiak, Andrzej
    HetR is an essential regulator of heterocyst development in cyanobacteria. HetR binds to a DNA palindrome upstream of the hetP gene. We report the crystal structure of HetR from Fischerella at 3.0 Å. The protein is a dimer comprised of a central DNA-binding unit containing the N-terminal regions of the two subunits organized with two helix-turn-helix motifs; two globular flaps extending in opposite directions; and a hood over the central core formed from the C-terminal subdomains. The flaps and hood have no structural precedent in the protein database, therefore representing new folds. The structural assignments are supported by sitedirected mutagenesis and DNA-binding studies. We suggest that HetR serves as a scaffold for assembly of transcription components critical for heterocyst development.
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    Recruitment in the sea: bacterial genes required for inducing larval settlement in a polychaete worm
    (Nature, 2012-01) Huang, Ying ; Callahan, Sean M. ; Hadfield, Michael G.
    Metamorphically competent larvae of the marine tubeworm Hydroides elegans can be induced to metamorphose by biofilms of the bacterium Pseudoalteromonas luteoviolacea strain HI1. Mutational analysis was used to identify four genes that are necessary for metamorphic induction and encode functions that may be related to cell adhesion and bacterial secretion systems. No major differences in biofilm characteristics, such as biofilm cell density, thickness, biomass and EPS biomass, were seen between biofilms composed of P. luteoviolacea (HI1) and mutants lacking one of the four genes. The analysis indicates that factors other than those relating to physical characteristics of biofilms are critical to the inductive capacity of P. luteoviolacea (HI1), and that essential inductive molecular components are missing in the non-inductive deletion-mutant strains.