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https://www.readbyqxmd.com/read/27911809/unique-attributes-of-cyanobacterial-metabolism-revealed-by-improved-genome-scale-metabolic-modeling-and-essential-gene-analysis
#1
Jared T Broddrick, Benjamin E Rubin, David G Welkie, Niu Du, Nathan Mih, Spencer Diamond, Jenny J Lee, Susan S Golden, Bernhard O Palsson
The model cyanobacterium, Synechococcus elongatus PCC 7942, is a genetically tractable obligate phototroph that is being developed for the bioproduction of high-value chemicals. Genome-scale models (GEMs) have been successfully used to assess and engineer cellular metabolism; however, GEMs of phototrophic metabolism have been limited by the lack of experimental datasets for model validation and the challenges of incorporating photon uptake. Here, we develop a GEM of metabolism in S. elongatus using random barcode transposon site sequencing (RB-TnSeq) essential gene and physiological data specific to photoautotrophic metabolism...
December 1, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27911807/enhanced-limonene-production-in-cyanobacteria-reveals-photosynthesis-limitations
#2
Xin Wang, Wei Liu, Changpeng Xin, Yi Zheng, Yanbing Cheng, Su Sun, Runze Li, Xin-Guang Zhu, Susie Y Dai, Peter M Rentzepis, Joshua S Yuan
Terpenes are the major secondary metabolites produced by plants, and have diverse industrial applications as pharmaceuticals, fragrance, solvents, and biofuels. Cyanobacteria are equipped with efficient carbon fixation mechanism, and are ideal cell factories to produce various fuel and chemical products. Past efforts to produce terpenes in photosynthetic organisms have gained only limited success. Here we engineered the cyanobacterium Synechococcus elongatus PCC 7942 to efficiently produce limonene through modeling guided study...
November 23, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27910631/a-simple-approach-to-spectrally-resolved-fluorescence-and-bright-field-microscopy-over-select-regions-of-interest
#3
Peter D Dahlberg, Christopher T Boughter, Nabil F Faruk, Lu Hong, Young Hoon Koh, Matthew A Reyer, Alon Shaiber, Aiman Sherani, Jiacheng Zhang, Justin E Jureller, Adam T Hammond
A standard wide field inverted microscope was converted to a spatially selective spectrally resolved microscope through the addition of a polarizing beam splitter, a pair of polarizers, an amplitude-mode liquid crystal-spatial light modulator, and a USB spectrometer. The instrument is capable of simultaneously imaging and acquiring spectra over user defined regions of interest. The microscope can also be operated in a bright-field mode to acquire absorption spectra of micron scale objects. The utility of the instrument is demonstrated on three different samples...
November 2016: Review of Scientific Instruments
https://www.readbyqxmd.com/read/27909431/the-microbiota-of-recreational-freshwaters-and-the-implications-for-environmental-and-public-health
#4
Chang Soo Lee, Minseok Kim, Cheonghoon Lee, Zhongtang Yu, Jiyoung Lee
The microbial communities in recreational freshwaters play important roles in both environmental and public health perspectives. In this study, the bacterial community structure and its associations with freshwater environments were investigated by analyzing the summertime microbiomes of three beach waters in Ohio (East Fork, Delaware, and Madison lakes) together with environmental and microbial water quality parameters. From the swimming season of 2009, 21 water samples were collected from the three freshwater beaches...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27908241/molecular-cloning-biochemical-characterization-and-antitumor-properties-of-a-novel-l-asparaginase-from-synechococcus-elongatus-pcc6803
#5
R Kebeish, A El-Sayed, H Fahmy, A Abdel-Ghany
L-asparaginase (EC 3.5.1.1), which catalyzes the deamidation of L-asparagine to L-aspartic acid and ammonia, has been widely used as a key therapeutic tool in the treatment of tumors. The current commercially available L-asparaginases, produced from bacteria, have signs of toxicity and hypersensitivity reactions during the course of tumor therapy. Therefore, searching for L-asparaginases with unique biochemical properties and fewer adverse effects was the objective of this work. In this study, cyanobacterial strain Synechococcus elongatus PCC6803 was found as a novel source of L-asparaginase...
October 2016: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/27905613/unambiguous-identification-and-discovery-of-bacterial-siderophores-by-direct-injection-21-tesla-fourier-transform-ion-cyclotron-resonance-mass-spectrometry
#6
Lawrence R Walker, Malak M Tfaily, Jared B Shaw, Nancy J Hess, Ljiljana Paša-Tolić, David W Koppenaal
Under iron-limiting conditions, bacteria produce low molecular mass Fe(iii) binding molecules known as siderophores to sequester the Fe(iii), along with other elements, increasing their bioavailability. Siderophores are thought to influence iron cycling and biogeochemistry in both marine and terrestrial ecosystems and hence the need for rapid, confident characterization of these compounds has increased. In this study, the type of siderophores produced by two marine bacterial species, Synechococcus sp. PCC 7002 and Vibrio cyclitrophicus 1F53, were characterized by use of a newly developed 21 T Fourier Transform Ion Cyclotron Resonance Mass Spectrometer (FTICR MS) with direct injection electrospray ionization...
December 1, 2016: Metallomics: Integrated Biometal Science
https://www.readbyqxmd.com/read/27902440/synechococcus-diversity-along-a-trophic-gradient-in-the-osterseen-lake-district-bavaria
#7
Joachim Ruber, Franziska Bauer, Andrew Millard, Uta Raeder, Jürgen Geist, Katrin Zwirglmaier
Picocyanobacteria are important primary producers in freshwater, however there is still a knowledge gap regarding their diversity at the strain level. For this reason, the microbial diversity of four lakes with different trophic states was investigated by sequencing of the 16S rRNA gene using universal primers. The study was performed in selected lakes of the Osterseen Lake District, Germany, from 2012 to 2014 (Lake Schiffhuettensee: eutrophic; Lake Ostersee: meso-oligotrophic; Lake Groebensee: oligotrophic; Lake Lustsee: oligotrophic)...
November 1, 2016: Microbiology
https://www.readbyqxmd.com/read/27902432/self-replicating-shuttle-vectors-based-on-pans-a-small-endogenous-plasmid-of-the-unicellular-cyanobacterium-synechococcus-elongatus-pcc-7942
#8
You Chen, Arnaud Taton, Michaela Go, Ross E London, Lindsey M Pieper, Susan S Golden, James W Golden
To facilitate development of synthetic biology tools for genetic engineering of cyanobacterial strains, we constructed pANS-derived self-replicating shuttle vectors that are based on the minimal replication element of the Synechococcus elongatus strain PCC 7942 plasmid pANS. To remove the possibility of homologous recombination events between the shuttle plasmids and the native pANS plasmid, the endogenous pANS was cured through plasmid incompatibility-mediated spontaneous loss. A heterologous toxin-antitoxin cassette was incorporated into the shuttle vectors for stable plasmid maintenance in the absence of antibiotic selection...
October 14, 2016: Microbiology
https://www.readbyqxmd.com/read/27891682/robust-min-system-oscillation-in-the-presence-of-internal-photosynthetic-membranes-in-cyanobacteria
#9
Joshua S MacCready, Jory Schossau, Katherine W Osteryoung, Daniel C Ducat
The oscillatory Min system of Escherichia coli defines the cell division plane by regulating the site of FtsZ-ring formation and represents one of the best-understood examples of emergent protein self-organization in nature. The oscillatory patterns of the Min-system proteins MinC, MinD and MinE (MinCDE) are strongly dependent on the geometry of membranes they bind. Complex internal membranes within cyanobacteria could disrupt this self-organization by sterically occluding or sequestering MinCDE from the plasma membrane...
November 5, 2016: Molecular Microbiology
https://www.readbyqxmd.com/read/27888364/in-vitro-reconstitution-of-the-cyclosporine-specific-p450-hydroxylases-using-heterologous-redox-partner-proteins
#10
Yue Sun, Li Ma, Dongfei Han, Lei Du, Fengxia Qi, Wei Zhang, Jingran Sun, Shan Huang, Eung-Soo Kim, Shengying Li
The cytochrome P450 enzymes (CYPs) CYP-sb21 from Sebekia benihana and CYP-pa1 from Pseudonocardia autotrophica are able to hydroxylate the immunosuppressant cyclosporin A (CsA) in a regioselective manner, giving rise to the production of two hair-stimulating agents (with dramatically attenuated immunosuppressant activity), γ-hydroxy-N-methyl-L-Leu4-CsA (CsA-4-OH) and γ-hydroxy-N-methyl-L-Leu9-CsA (CsA-9-OH). Recently, the in vitro activity of CYP-sb21 was identified using several surrogate redox partner proteins...
November 25, 2016: Journal of Industrial Microbiology & Biotechnology
https://www.readbyqxmd.com/read/27884049/copper-toxicity-response-influences-mesotrophic-synechococcus-community-structure
#11
Rhona K Stuart, Randelle Bundy, Kristen Buck, Majid Ghassemain, Kathy Barbeau, Brian Palenik
Picocyanobacteria from the genus Synechococcus are ubiquitous in ocean waters. Their phylogenetic and genomic diversity suggests ecological niche differentiation, but the selective forces influencing this are not well defined. Marine picocyanobacteria are sensitive to Cu toxicity, so adaptations to this stress could represent a selective force within, and between, "species" also known as clades. We compared Cu stress responses in cultures and natural populations of marine Synechococcus from two co-occurring major mesotrophic clades (I and IV)...
November 24, 2016: Environmental Microbiology
https://www.readbyqxmd.com/read/27881980/comparative-genomics-of-dna-recombination-and-repair-in-cyanobacteria-biotechnological-implications
#12
REVIEW
Corinne Cassier-Chauvat, Théo Veaudor, Franck Chauvat
Cyanobacteria are fascinating photosynthetic prokaryotes that are regarded as the ancestors of the plant chloroplast; the purveyors of oxygen and biomass for the food chain; and promising cell factories for an environmentally friendly production of chemicals. In colonizing most waters and soils of our planet, cyanobacteria are inevitably challenged by environmental stresses that generate DNA damages. Furthermore, many strains engineered for biotechnological purposes can use DNA recombination to stop synthesizing the biotechnological product...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27878952/newly-isolated-nodularia-phage-influences-cyanobacterial-community-dynamics
#13
S E Coloma, A Dienstbier, D H Bamford, K Sivonen, E Roine, T Hiltunen
Cyanophages, i.e. viruses infecting cyanobacteria, are a key component driving cyanobacterial community dynamics both ecologically and evolutionarily. In addition to reducing biomass and influencing the genetic diversity of their host populations, they can also have a wider community-level impact due to the release of nutrients by phage-induced cell lysis. In this study, we isolated and characterized a new cyanophage, a siphophage designated as vB_NpeS-2AV2, capable of infecting the filamentous nitrogen fixing cyanobacterium Nodularia sp...
November 23, 2016: Environmental Microbiology
https://www.readbyqxmd.com/read/27871145/meta-omic-analyses-of-baltic-sea-cyanobacteria-diversity-community-structure-and-salt-acclimation
#14
Narin Celepli, John Sundh, Martin Ekman, Chris L Dupont, Shibu Yooseph, Birgitta Bergman, Karolina Ininbergs
Cyanobacteria are important phytoplankton in the Baltic Sea, an estuarine-like environment with pronounced north to south gradient in salinity and nutrient concentrations. Here we present a metagenomic and -transcriptomic survey, with subsequent analyses targeting the genetic identity, phylogenetic diversity, and spatial distribution of Baltic Sea cyanobacteria. The cyanobacterial community constituted close to 12% of the microbial population sampled during a pre-bloom period (June-July 2009). The community was dominated by unicellular picocyanobacteria, specifically a few highly abundant taxa (Synechococcus and Cyanobium) with a long tail of low abundance representatives, and local peaks of bloom-forming heterocystous taxa...
November 21, 2016: Environmental Microbiology
https://www.readbyqxmd.com/read/27867760/pico-and-nanoplankton-abundance-and-carbon-stocks-along-the-brazilian-bight
#15
Catherine Gérikas Ribeiro, Adriana Lopes Dos Santos, Dominique Marie, Vivian Helena Pellizari, Frederico Pereira Brandini, Daniel Vaulot
Pico and nanoplankton communities from the Southwest Atlantic Ocean along the Brazilian Bight are poorly described. The hydrography in this region is dominated by a complex system of layered water masses, which includes the warm and oligotrophic Tropical Water (TW), the cold and nutrient rich South Atlantic Central Water (SACW) and the Coastal Water (CW), which have highly variable properties. In order to assess how pico- and nanoplankton communities are distributed in these different water masses, we determined by flow cytometry the abundance of heterotrophic bacteria, Prochlorococcus, Synechococcus and autotrophic pico and nanoeukaryotes along three transects, extending from 23°S to 31°S and 39°W to 49°W...
2016: PeerJ
https://www.readbyqxmd.com/read/27862807/microbial-processes-of-the-carbon-and-sulfur-cycles-in-an-ice-covered-iron-rich-meromictic-lake-svetloe-arkhangelsk-region-russia
#16
Alexander S Savvichev, Natalia M Kokryatskaya, Svetlana A Zabelina, Igor I Rusanov, Elena E Zakharova, Elena F Veslopolova, Olga N Lunina, Ekaterina O Patutina, Boris K Bumazhkin, Denis S Gruzdev, Pavel A Sigalevich, Nikolay V Pimenov, Boris B Kuznetsov, Vladimir M Gorlenko
Biogeochemical, isotope geochemical, and microbiological investigation of Lake Svetloe (White Sea basin), a meromictic freshwater was carried out in April 2014, when ice thickness was ∼0.5 m, and the ice-covered water column contained oxygen to 23-m depth. Below, the anoxic water column contained ferrous iron (up to 240 µM), manganese (60 µM), sulfide (up to 2 µM), and dissolved methane (960 µM). The highest abundance of microbial cells revealed by epifluorescence microscopy was found in the chemocline (redox zone) at 23-24...
November 16, 2016: Environmental Microbiology
https://www.readbyqxmd.com/read/27856621/trophic-state-and-geographic-gradients-influence-planktonic-cyanobacterial-diversity-and-distribution-in-new-zealand-lakes
#17
Susanna A Wood, Marcia Y Maier, Jonathan Puddick, Xavier Pochon, Anastasija Zaiko, Daniel R Dietrich, David P Hamilton
Cyanobacteria are commonly associated with eutrophic lakes, where they often form blooms and produce toxins. However they are a ubiquitous component of phytoplankton in lakes of widely varying trophic status. We hypothesised that cyanobacterial diversity would vary among lakes of differing trophic status, but that the relative importance of geographic and hydromorphological characteristics driving these patterns would differ across trophic groups. DNA from 143 New Zealand lakes that spanned a range of geographic, hydromorphological and trophic gradients was analysed using automated rRNA intergenic spacer analysis (ARISA) and screened for genes involved in cyanotoxin production...
November 16, 2016: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/27846887/crispr-interference-crispri-for-gene-regulation-and-succinate-production-in-cyanobacterium-s-elongatus-pcc-7942
#18
Chun-Hung Huang, Claire R Shen, Hung Li, Li-Yu Sung, Meng-Ying Wu, Yu-Chen Hu
BACKGROUND: Cyanobacterium Synechococcus elongatus PCC 7942 holds promise for biochemical conversion, but gene deletion in PCC 7942 is time-consuming and may be lethal to cells. CRISPR interference (CRISPRi) is an emerging technology that exploits the catalytically inactive Cas9 (dCas9) and single guide RNA (sgRNA) to repress sequence-specific genes without the need of gene knockout, and is repurposed to rewire metabolic networks in various procaryotic cells. RESULTS: To employ CRISPRi for the manipulation of gene network in PCC 7942, we integrated the cassettes expressing enhanced yellow fluorescent protein (EYFP), dCas9 and sgRNA targeting different regions on eyfp into the PCC 7942 chromosome...
November 15, 2016: Microbial Cell Factories
https://www.readbyqxmd.com/read/27846565/physiological-and-ecological-drivers-of-early-spring-blooms-of-a-coastal-phytoplankter
#19
Kristen R Hunter-Cevera, Michael G Neubert, Robert J Olson, Andrew R Solow, Alexi Shalapyonok, Heidi M Sosik
Climate affects the timing and magnitude of phytoplankton blooms that fuel marine food webs and influence global biogeochemical cycles. Changes in bloom timing have been detected in some cases, but the underlying mechanisms remain elusive, contributing to uncertainty in long-term predictions of climate change impacts. Here we describe a 13-year hourly time series from the New England shelf of data on the coastal phytoplankter Synechococcus, during which the timing of its spring bloom varied by 4 weeks. We show that multiyear trends are due to temperature-induced changes in cell division rate, with earlier blooms driven by warmer spring water temperatures...
October 21, 2016: Science
https://www.readbyqxmd.com/read/27837093/variety-of-dna-replication-activity-among-cyanobacteria-correlates-with-distinct-respiration-activity-in-the-dark
#20
Ryudo Ohbayashi, Jun-Ya Yamamoto, Satoru Watanabe, Yu Kanesaki, Taku Chibazakura, Shin-Ya Miyagishima, Hirofumi Yoshikawa
Cyanobacteria exhibit light-dependent cell growth since most of their cellular energy is obtained by photosynthesis. In Synechococcus elongatus PCC 7942, one of the model cyanobacterium, DNA replication depends on the photosynthetic electron transport. However, the critical signal for regulatory mechanism of DNA replication has not been identified. In addition, conservation of this regulatory mechanism has not been investigated among cyanobacteria. To understand this regulatory signal and its dependence on light, we examined the regulation of DNA replication under both light and dark condition among three model cyanobacteria, S...
November 10, 2016: Plant & Cell Physiology
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