Kuo Alan J.

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Kuo
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Alan J.
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  • Thesis
    Mutant analysis of luminescence and autoinduction in a marine bacterium
    (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 1994-12) Kuo, Alan J.
    The marine symbiotic bacterium Vibrio fischeri is striking for its ability both to emit light and to dramatically regulate light emission using a cell-to-cell signalling mechanism called autoinduction. The latter is mediated by a signal molecule called the "autoinducer". The mechanistic bases of both luminescence and autoinduction are well known in V. fischeri, but this knowledge is mostly derived from studies of the cloned luminescence and autoinduction genes expressed in Escherichia coli. In this study, luminescence and autoinduction mutations were systematically generated in V. fischeri to explore aspects of luminescence and autoinduction not addressable in E. coli, such as the adaptive significance of luminescence. Most dramatically, the mutants revealed the presence of multiple autoinducers and autoinducer synthases in V. fischeri. One of the autoinducers (autoinducer-2, or AI-2) was chemically purified and shown to be Noctanoyi- L-homoserine lactone. The genetic locus encoding the AI-2 synthase was cloned and designated ain (autoinducer). Manipulation of ain and AI-2 in V. jischeri demonstrated that the function of AI-2 appears to be to inhibit rather than to promote autoinduction.
  • Preprint
    Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics
    ( 2011-01) Gobler, Christopher J. ; Berry, Dianna L. ; Dyhrman, Sonya T. ; Wilhelm, Steven W. ; Salamov, Asaf ; Lobanov, Alexei V. ; Zhang, Yan ; Collier, Jackie L. ; Wurch, Louie L. ; Kustka, Adam B. ; Dill, Brian D. ; Shah, Manesh ; VerBerkmoes, Nathan C. ; Kuo, Alan J. ; Terry, Astrid ; Pangilinan, Jasmyn ; Lindquist, Erika A. ; Lucas, Susan ; Paulsen, Ian T. ; Hattenrath-Lehmann, Theresa K. ; Talmage, Stephanie C. ; Walker, Elyse A. ; Koch, Florian ; Burson, Amanda M. ; Marcoval, Maria Alejandra ; Tang, Ying-Zhong ; LeCleir, Gary R. ; Coyne, Kathryn J. ; Berg, Gry M. ; Bertrand, Erin M. ; Saito, Mak A. ; Gladyshev, Vadim N. ; Grigoriev, Igor V.
    Harmful algal blooms (HABs) cause significant economic and ecological damage worldwide. Despite considerable efforts, a comprehensive understanding of the factors that promote these blooms has been lacking because the biochemical pathways that facilitate their dominance relative to other phytoplankton within specific environments have not been identified. Here, biogeochemical measurements demonstrated that the harmful 43 Aureococcus anophagefferens outcompeted co-occurring phytoplankton in estuaries with elevated levels of dissolved organic matter and turbidity and low levels of dissolved inorganic nitrogen. We subsequently sequenced the first HAB genome (A. anophagefferens) and compared its gene complement to those of six competing phytoplankton species identified via metaproteomics. Using an ecogenomic approach, we specifically focused on the gene sets that may facilitate dominance within the environmental conditions present during blooms. A. anophagefferens possesses a larger genome (56 mbp) and more genes involved in light harvesting, organic carbon and nitrogen utilization, and encoding selenium- and metal-requiring enzymes than competing phytoplankton. Genes for the synthesis of microbial deterrents likely permit the proliferation of this species with reduced mortality losses during blooms. Collectively, these findings suggest that anthropogenic activities resulting in elevated levels of turbidity, organic matter, and metals have opened a niche within coastal ecosystems that ideally suits the unique genetic capacity of A. anophagefferens and thus has facilitated the proliferation of this and potentially other HABs.
  • Article
    Pan genome of the phytoplankton Emiliania underpins its global distribution
    (Nature Publishing Group, 2013-07-10) Read, Betsy A. ; Kegel, Jessica ; Klute, Mary J. ; Kuo, Alan J. ; Lefebvre, Stephane C. ; Maumus, Florian ; Mayer, Christoph ; Miller, John ; Monier, Adam ; Salamov, Asaf ; Young, Jeremy ; Aguilar, Maria ; Claverie, Jean-Michel ; Frickenhaus, Stephan ; Gonzalez, Karina ; Herman, Emily K. ; Lin, Yao-Cheng ; Napier, Johnathan ; Ogata, Hiroyuki ; Sarno, Analissa F. ; Shmutz, Jeremy ; Schroeder, Declan C. ; de Vargas, Colomban ; Verret, Frederic ; von Dassow, Peter ; Valentin, Klaus ; Van de Peer, Yves ; Wheeler, Glen L. ; Emiliania huxleyi Annotation Consortium ; Dacks, Joel B. ; Delwiche, Charles F. ; Dyhrman, Sonya T. ; Glockne, Gernot ; Joh, Uwe ; Richards, Thomas ; Worden, Alexandra Z. ; Zhang, Xiaoyu ; Grigoriev, Igor V.
    Coccolithophores have influenced the global climate for over 200 million years1. These marine phytoplankton can account for 20 per cent of total carbon fixation in some systems2. They form blooms that can occupy hundreds of thousands of square kilometres and are distinguished by their elegantly sculpted calcium carbonate exoskeletons (coccoliths), rendering them visible from space3. Although coccolithophores export carbon in the form of organic matter and calcite to the sea floor, they also release CO2 in the calcification process. Hence, they have a complex influence on the carbon cycle, driving either CO2 production or uptake, sequestration and export to the deep ocean4. Here we report the first haptophyte reference genome, from the coccolithophore Emiliania huxleyi strain CCMP1516, and sequences from 13 additional isolates. Our analyses reveal a pan genome (core genes plus genes distributed variably between strains) probably supported by an atypical complement of repetitive sequence in the genome. Comparisons across strains demonstrate that E. huxleyi, which has long been considered a single species, harbours extensive genome variability reflected in different metabolic repertoires. Genome variability within this species complex seems to underpin its capacity both to thrive in habitats ranging from the equator to the subarctic and to form large-scale episodic blooms under a wide variety of environmental conditions.