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https://www.readbyqxmd.com/read/28799725/engineering-of-corynebacterium-glutamicum-for-consolidated-conversion-of-hemicellulosic-biomass-into-xylonic-acid
#1
Sung Sun Yim, Jae Woong Choi, Se Hwa Lee, Eun Jung Jeon, Wook-Jin Chung, Ki Jun Jeong
Xylonic acid is a promising platform chemical with various applications in the fields of food, pharmaceuticals, and agriculture. However, in the current process, xylonic acid is mainly produced by the conversion of xylose, whose preparation requires substantial cost and time. Here, we engineered Corynebacterium glutamicum for the consolidated bioconversion of hemicellulosic biomass (xylan) into xylonic acid in a single cultivation. First, for the efficient conversion of xylose to xylonic acid, xylose dehydrogenase (Xdh) and xylonolactonase (XylC) from Caulobacter crescentus were evaluated together with a previously optimized xylose transporter module (XylE of Escherichia coli), and cells expressing xdh and xylE genes with an optimized expression system could produce xylonic acid from xylose with 100% conversion yield...
August 11, 2017: Biotechnology Journal
https://www.readbyqxmd.com/read/28768811/conformational-and-chemical-selection-by-a-trans-acting-editing-domain
#2
Eric M Danhart, Marina Bakhtina, William A Cantara, Alexandra B Kuzmishin, Xiao Ma, Brianne L Sanford, Marija Košutić, Yuki Goto, Hiroaki Suga, Kotaro Nakanishi, Ronald Micura, Mark P Foster, Karin Musier-Forsyth
Molecular sieves ensure proper pairing of tRNAs and amino acids during aminoacyl-tRNA biosynthesis, thereby avoiding detrimental effects of mistranslation on cell growth and viability. Mischarging errors are often corrected through the activity of specialized editing domains present in some aminoacyl-tRNA synthetases or via single-domain trans-editing proteins. ProXp-ala is a ubiquitous trans-editing enzyme that edits Ala-tRNA(Pro), the product of Ala mischarging by prolyl-tRNA synthetase, although the structural basis for discrimination between correctly charged Pro-tRNA(Pro) and mischarged Ala-tRNA(Ala) is unclear...
August 15, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28737755/biphasic-growth-dynamics-control-cell-division-in-caulobacter-crescentus
#3
Shiladitya Banerjee, Klevin Lo, Matthew K Daddysman, Alan Selewa, Thomas Kuntz, Aaron R Dinner, Norbert F Scherer
Cell size is specific to each species and impacts cell function. Various phenomenological models for cell size regulation have been proposed, but recent work in bacteria has suggested an 'adder' model, in which a cell increments its size by a constant amount between each division. However, the coupling between cell size, shape and constriction remains poorly understood. Here, we investigate size control and the cell cycle dependence of bacterial growth using multigenerational cell growth and shape data for single Caulobacter crescentus cells...
July 24, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28697666/bacterial-cell-division-nonmodels-poised-to-take-the-spotlight
#4
Prahathees J Eswara, Kumaran S Ramamurthi
The last three decades have witnessed an explosion of discoveries about the mechanistic details of binary fission in model bacteria such as Escherichia coli, Bacillus subtilis, and Caulobacter crescentus. This was made possible not only by advances in microscopy that helped answer questions about cell biology but also by clever genetic manipulations that directly and easily tested specific hypotheses. More recently, research using understudied organisms, or nonmodel systems, has revealed several alternate mechanistic strategies that bacteria use to divide and propagate...
July 11, 2017: Annual Review of Microbiology
https://www.readbyqxmd.com/read/28661661/caulobacter-crescentus-cell-cycle-regulated-dna-methyltransferase-uses-a-novel-mechanism-for-substrate-recognition
#5
COMPARATIVE STUDY
Clayton B Woodcock, Aziz B Yakubov, Norbert O Reich
Caulobacter crescentus relies on DNA methylation by the cell cycle-regulated methyltransferase (CcrM) in addition to key transcription factors to control the cell cycle and direct cellular differentiation. CcrM is shown here to efficiently methylate its cognate recognition site 5'-GANTC-3' in single-stranded and hemimethylated double-stranded DNA. We report the Km, kcat, kmethylation, and Kd for single-stranded and hemimethylated substrates, revealing discrimination of 10(7)-fold for noncognate sequences. The enzyme also shows a similar discrimination against single-stranded RNA...
August 1, 2017: Biochemistry
https://www.readbyqxmd.com/read/28630129/polar-organizing-protein-popz-is-required-for-chromosome-segregation-in-agrobacterium-tumefaciens
#6
Haley M Ehrle, Jacob T Guidry, Rebecca Iacovetto, Anne K Salisbury, D J Sandidge, Grant R Bowman
Despite being perceived as relatively simple organisms, many bacteria exhibit an impressive degree of subcellular 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...
September 1, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28630123/absence-of-the-polar-organizing-protein-popz-results-in-reduced-and-asymmetric-cell-division-in-agrobacterium-tumefaciens
#7
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 midcell 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...
September 1, 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
#8
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
#9
Selamawit Abi 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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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...
August 30, 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
#16
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
#17
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, whereas 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...
June 30, 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
#18
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
#19
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
#20
Alexandra Males, Lluís Raich, Spencer J Williams, Carme Rovira, Gideon J Davies
The varied yet family-specific conformational pathways used by individual glycoside hydrolases (GHs) offer a tantalising prospect for the design of tightly 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 that is selective for GH family 47 inverting α-mannosidases. Here we show, through quantum-mechanical approaches, that kifunensine is restrained to a "ring-flipped" (1) C4 conformation with another accessible, but higher-energy, region around the (1,4) B conformation...
May 11, 2017: Chembiochem: a European Journal of Chemical Biology
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