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https://www.readbyqxmd.com/read/28630129/the-polar-organizing-protein-popz-is-required-for-chromosome-segregation-in-agrobacterium-tumefaciens
#1
Haley M Ehrle, Jacob T Guidry, Rebecca Iacovetto, Anne K Salisbury, D J Sandidge, Grant Bowman
Despite being perceived as relatively simple organisms, many bacteria exhibit an impressive degree of sub-cellular organization. In Caulobacter crescentus, the evolutionarily conserved polar organizing protein PopZ facilitates cytoplasmic organization by recruiting chromosome centromeres and regulatory proteins to the cell poles. Here, we characterize the localization and function of PopZ in Agrobacterium tumefaciens, a genetically related species with distinct anatomy. In this species, we find that PopZ molecules are relocated from the old pole to the new pole in the minutes following cell division...
June 19, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28630123/absence-of-the-polar-organizing-protein-popz-causes-aberrant-cell-division-in-agrobacterium-tumefaciens
#2
Matthew Howell, Alena Aliashkevich, Anne K Salisbury, Felipe Cava, Grant R Bowman, Pamela J B Brown
Agrobacterium tumefaciens is a rod-shaped bacterium that grows by polar insertion of new peptidoglycan during cell elongation. As the cell cycle progresses, peptidoglycan synthesis at the pole ceases prior to insertion of new peptidoglycan at mid-cell to enable cell division. The A. tumefaciens homolog of the Caulobacter crescentus polar organelle development protein PopZ has been identified as a growth pole marker and a candidate polar growth promoting factor. Here, we characterize the function of PopZ in cell growth and division of A...
June 19, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28627757/super-resolution-microscopy-and-single-protein-tracking-in-live-bacteria-using-a-genetically-encoded-photostable-fluoromodule
#3
Saumya Saurabh, Adam M Perez, Colin J Comerci, Lucy Shapiro, W E Moerner
Visualization of dynamic protein structures in live cells is crucial for understanding the mechanisms governing biological processes. Fluorescence microscopy is a sensitive tool for this purpose. In order to image proteins in live bacteria using fluorescence microscopy, one typically genetically fuses the protein of interest to a photostable fluorescent tag. Several labeling schemes are available to accomplish this. Particularly, hybrid tags that combine a fluorescent or fluorogenic dye with a genetically encoded protein (such as enzymatic labels) have been used successfully in multiple cell types...
June 19, 2017: Current Protocols in Cell Biology
https://www.readbyqxmd.com/read/28613431/a-conserved-coiled-coil-protein-pair-focuses-the-cytokinetic-z-ring-in-caulobacter-crescentus
#4
Selamawit Woldemeskel, Ryan McQuillen, Alex M Hessel, Jie Xiao, Erin D Goley
The cytoskeletal GTPase FtsZ assembles at midcell, recruits the division machinery, and directs envelope invagination for bacterial cytokinesis. ZapA, a conserved FtsZ-binding protein, promotes Z-ring stability and efficient division through a mechanism that is not fully understood. Here we investigated the function of ZapA in Caulobacter crescentus. We found that ZapA is encoded in an operon with a small coiled-coil protein we named ZauP. ZapA and ZauP co-localized at the division site and were each required for efficient division...
June 14, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28598303/caulobacter-rhizosphaerae-sp-nov-a-stalked-bacterium-isolated-from-rhizosphere-soil
#5
Le-Ni Sun, En-Dong Yang, Xue-Ting Hou, Jie-Chao Wei, Zhuo-Xin Yuan, Wei-Yun Wang
The Gram-reaction-negative, aerobic, white- to pale-yellow-coloured and rod-shaped bacterium with a single polar flagellum or a stalk, designated strain 7F14T, was isolated from rhizosphere soil of cultivated watermelon (Citrullus lanatus) collected from Hefei, China. Growth of strain 7F14T was observed at pH 6.0-9.0, 10-30 °C and in the presence of 0-1 % (w/v) NaCl. Cells were catalase-negative and oxidase-positive. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain 7F14T formed a phyletic lineage within the genus Caulobacter of the family Caulobacteraceae and showed the highest 16S rRNA gene sequence similarities to Caulobacter henricii ATCC 15253T (98...
June 9, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28593654/linkage-of-microbial-kinetics-and-bacterial-community-structure-of-mbr-and-hybrid-mbbr-mbr-systems-to-treat-salinity-amended-urban-wastewater
#6
Alejandro Rodriguez-Sanchez, Juan Carlos Leyva-Diaz, Alejandro Gonzalez-Martinez, Jose Manuel Poyatos
Three pilot-scale bioreactors were started up and operated under salinity-amended urban wastewater feeding. The bioreactors were configured as membrane bioreactor and two different hybrid, moving bed biofilm reactor-membrane bioreactor and operated with a hydraulic retention time of 9.5 h, a solid residence time of 11.75 days and a total solids concentration of 2500 mg L(-1) . The three systems showed excellent performance in suspended solids, BOD5 , and COD removal (values of 96-100%, 97-99%, and 88-90%, respectively), but poor nitrogen removal (values of 20-30%)...
June 8, 2017: Biotechnology Progress
https://www.readbyqxmd.com/read/28591613/analysis-of-noise-mechanisms-in-cell-size-control
#7
Saurabh Modi, Cesar Augusto Vargas-Garcia, Khem Raj Ghusinga, Abhyudai Singh
At the single-cell level, noise arises from multiple sources, such as inherent stochasticity of biomolecular processes, random partitioning of resources at division, and fluctuations in cellular growth rates. How these diverse noise mechanisms combine to drive variations in cell size within an isoclonal population is not well understood. Here, we investigate the contributions of different noise sources in well-known paradigms of cell-size control, such as adder (division occurs after adding a fixed size from birth), sizer (division occurs after reaching a size threshold), and timer (division occurs after a fixed time from birth)...
June 6, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28552553/large-scale-chromosome-folding-versus-genomic-dna-sequences-a-discrete-double-fourier-transform-technique
#8
V R Chechetkin, V V Lobzin
Using state-of-the-art techniques combining imaging methods and high-throughput genomic mapping tools leaded to the significant progress in detailing chromosome architecture of various organisms. However, a gap still remains between the rapidly growing structural data on the chromosome folding and the large-scale genome organization. Could a part of information on the chromosome folding be obtained directly from underlying genomic DNA sequences abundantly stored in the databanks? To answer this question, we developed an original discrete double Fourier transform (DDFT)...
May 26, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28536693/the-essential-role-of-clpxp-in-caulobacter-crescentus-requires-species-constrained-substrate-specificity
#9
Robert H Vass, Jacob Nascembeni, Peter Chien
The ClpXP protease is a highly conserved AAA+ degradation machine that is present throughout bacteria and in eukaryotic organelles. ClpXP is essential in some bacteria, such as Caulobacter crescentus, but dispensible in others, such as Escherichia coli. In Caulobacter, ClpXP normally degrades the SocB toxin and increased levels of SocB result in cell death. ClpX can be deleted in cells lacking this toxin, but these ΔclpX strains are still profoundly deficient in morphology and growth supporting the existence of additional important functions for ClpXP...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28533123/molecular-characterization-of-caulobacter-crescentus-mutator-strains
#10
Marinalva Martins-Pinheiro, Alice R Oliveira, Alexy O Valencia, Frank S Fernandez-Silva, Larissa G Silva, Carina O Lopes-Kulishev, Valeria C S Italiani, Marilis V Marques, Carlos F Menck, Rodrigo S Galhardo
Mutator strains were identified by screening random Tn5 insertion clones of Caulobacter crescentus. We identified clones with robust increases in mutation rates with Tn5 insertions in the mutY, mutS, mutL and uvrD genes, known to act in mutation-preventing pathways in Escherichia coli. Analysis of mutations in the rpoB gene revealed that in both the parental strain and mismatch repair-deficient mutants, A:T→G:C transitions predominate by a large margin over C:G→T:A. We have also investigated the role of the error-prone polymerase encoded by imuC (dnaE2) in spontaneous mutagenesis, and found that a imuC mutant strain shows mutation rates and sequences comparable to the parental strain...
May 19, 2017: Gene
https://www.readbyqxmd.com/read/28531174/genome-partitioner-a-web-tool-for-multi-level-partitioning-of-large-scale-dna-constructs-for-synthetic-biology-applications
#11
Matthias Christen, Luca Del Medico, Heinz Christen, Beat Christen
Recent advances in lower-cost DNA synthesis techniques have enabled new innovations in the field of synthetic biology. Still, efficient design and higher-order assembly of genome-scale DNA constructs remains a labor-intensive process. Given the complexity, computer assisted design tools that fragment large DNA sequences into fabricable DNA blocks are needed to pave the way towards streamlined assembly of biological systems. Here, we present the Genome Partitioner software implemented as a web-based interface that permits multi-level partitioning of genome-scale DNA designs...
2017: PloS One
https://www.readbyqxmd.com/read/28507098/cargo-engagement-protects-protease-adaptors-from-degradation-in-a-substrate-specific-manner
#12
Kamal Kishore Joshi, Madeleine Sutherland, Peter Chien
Protein degradation in bacteria is a highly controlled process involving proteolytic adaptors that regulate protein degradation during cell cycle progression or during stress responses. Many adaptors work as scaffolds that selectively bind cargo and tether substrates to their cognate proteases to promote substrate destruction, while others primarily activate the target protease. Because adaptors must bind their cognate protease, all adaptors run the risk of being recognized by the protease as substrates themselves, a process that could limit their effectiveness...
May 15, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28500524/cytoskeletal-proteins-in-caulobacter-crescentus-spatial-orchestrators-of-cell-cycle-progression-development-and-cell-shape
#13
Kousik Sundararajan, Erin D Goley
Caulobacter crescentus, an aquatic Gram-negative α-proteobacterium, is dimorphic, as a result of asymmetric cell divisions that give rise to a free-swimming swarmer daughter cell and a stationary stalked daughter. Cell polarity of vibrioid C. crescentus cells is marked by the presence of a stalk at one end in the stationary form and a polar flagellum in the motile form. Progression through the cell cycle and execution of the associated morphogenetic events are tightly controlled through regulation of the abundance and activity of key proteins...
2017: Sub-cellular Biochemistry
https://www.readbyqxmd.com/read/28494955/environmental-calcium-controls-alternate-physical-states-of-the-caulobacter-surface-layer
#14
Jonathan Herrmann, Fatemeh Jabbarpour, Paul G Bargar, John F Nomellini, Po-Nan Li, Thomas J Lane, Thomas M Weiss, John Smit, Lucy Shapiro, Soichi Wakatsuki
Surface layers (S-layers) are paracrystalline, proteinaceous structures found in most archaea and many bacteria. Often the outermost cell envelope component, S-layers serve diverse functions including aiding pathogenicity and protecting against predators. We report that the S-layer of Caulobacter crescentus exhibits calcium-mediated structural plasticity, switching irreversibly between an amorphous aggregate state and the crystalline state. This finding invalidates the common assumption that S-layers serve only as static wall-like structures...
May 9, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28493500/conformational-analysis-of-the-mannosidase-inhibitor-kifunensine-a-quantum-mechanical-and-structural-approach
#15
Alexandra Males, Lluis Raich, Spencer J Williams, Carme Rovira, Gideon John Davies
The varied yet family-specific conformational pathways utilized by individual glycoside hydrolases (GHs) offer a tantalising prospect for the design of tight binding and specific enzyme inhibitors. A cardinal example of a GH family specific inhibitor, and one that finds widespread practical use, is the natural product kifunensine, which is a low nanomolar inhibitor selective for GH family 47 inverting a-mannosidases. Here we show, through quantum mechanical approaches, that kifunensine is restrained to a 'ring-flipped' 1C4 conformation with another accessible, but higher-energy, region around the 1,4B conformation...
May 11, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28489851/global-analysis-of-double-strand-break-processing-reveals-in-vivo-properties-of-the-helicase-nuclease-complex-addab
#16
Anjana Badrinarayanan, Tung B K Le, Jan-Hendrik Spille, Ibrahim I Cisse, Michael T Laub
In bacteria, double-strand break (DSB) repair via homologous recombination is thought to be initiated through the bi-directional degradation and resection of DNA ends by a helicase-nuclease complex such as AddAB. The activity of AddAB has been well-studied in vitro, with translocation speeds between 400-2000 bp/s on linear DNA suggesting that a large section of DNA around a break site is processed for repair. However, the translocation rate and activity of AddAB in vivo is not known, and how AddAB is regulated to prevent excessive DNA degradation around a break site is unclear...
May 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28443069/long-term-enrichment-of-stress-tolerant-cellulolytic-soil-populations-following-timber-harvesting-evidenced-by-multi-omic-stable-isotope-probing
#17
Roland C Wilhelm, Erick Cardenas, Hilary Leung, András Szeitz, Lionel D Jensen, William W Mohn
Soil management is vital for maintaining the productivity of commercial forests, yet the long-term impact of timber harvesting on soil microbial communities remains largely a matter of conjecture. Decomposition of plant biomass, comprised mainly of lignocellulose, has a broad impact on nutrient cycling, microbial activity and physicochemical characteristics of soil. At "Long-term Soil Productivity Study" sites in California dominated by Ponderosa pine, we tested whether clear-cut timber harvesting, accompanied by varying degrees of organic matter (OM) removal, affected the activity and structure of the cellulose-degrading microbial populations 16 years after harvesting...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28438890/short-ftsz-filaments-can-drive-asymmetric-cell-envelope-constriction-at-the-onset-of-bacterial-cytokinesis
#18
Qing Yao, Andrew I Jewett, Yi-Wei Chang, Catherine M Oikonomou, Morgan Beeby, Cristina V Iancu, Ariane Briegel, Debnath Ghosal, Grant J Jensen
FtsZ, the bacterial homologue of eukaryotic tubulin, plays a central role in cell division in nearly all bacteria and many archaea. It forms filaments under the cytoplasmic membrane at the division site where, together with other proteins it recruits, it drives peptidoglycan synthesis and constricts the cell. Despite extensive study, the arrangement of FtsZ filaments and their role in division continue to be debated. Here, we apply electron cryotomography to image the native structure of intact dividing cells and show that constriction in a variety of Gram-negative bacterial cells, including Proteus mirabilis and Caulobacter crescentus, initiates asymmetrically, accompanied by asymmetric peptidoglycan incorporation and short FtsZ-like filament formation...
June 1, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28425205/engineering-the-xylose-catabolizing-dahms-pathway-for-production-of-poly-d-lactate-co-glycolate-and-poly-d-lactate-co-glycolate-co-d-2-hydroxybutyrate-in-escherichia-coli
#19
So Young Choi, Won Jun Kim, Seung Jung Yu, Si Jae Park, Sung Gap Im, Sang Yup Lee
Poly(lactate-co-glycolate), PLGA, is a representative synthetic biopolymer widely used in medical applications. Recently, we reported one-step direct fermentative production of PLGA and its copolymers by metabolically engineered Escherichia coli from xylose and glucose. In this study, we report development of metabolically engineered E. coli strains for the production of PLGA and poly(d-lactate-co-glycolate-co-d-2-hydroxybutyrate) having various monomer compositions from xylose as a sole carbon source. To achieve this, the metabolic flux towards Dahms pathway was modulated using five different synthetic promoters for the expression of Caulobacter crescentus XylBC...
April 19, 2017: Microbial Biotechnology
https://www.readbyqxmd.com/read/28418382/structure-of-the-hexagonal-surface-layer-on-caulobacter-crescentus-cells
#20
Tanmay A M Bharat, Danguole Kureisaite-Ciziene, Gail G Hardy, Ellen W Yu, Jessica M Devant, Wim J H Hagen, Yves V Brun, John A G Briggs, Jan Löwe
Many prokaryotic cells are encapsulated by a surface layer (S-layer) consisting of repeating units of S-layer proteins. S-layer proteins are a diverse class of molecules found in Gram-positive and Gram-negative bacteria and most archaea(1-5). S-layers protect cells from the outside, provide mechanical stability and also play roles in pathogenicity. In situ structural information about this highly abundant class of proteins is scarce, so atomic details of how S-layers are arranged on the surface of cells have remained elusive...
April 18, 2017: Nature Microbiology
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