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Bo-Young Hong, Joseph N Paulson, O Colin Stine, George M Weinstock, Jorge L Cervantes
The lung microbiota has received less attention compared to other body sites, in part because its study carries special technological difficulties related to obtaining reliable samples as compared to other body niches. The limited number of studies on the sputum microbiota on TB patients and controls available so far have reported inconsistent, and sometimes, contradictory results. Aiming to clarify if changes in the lung microbiota composition are associated with pulmonary TB, we performed a meta-analysis of available data on microbiota of the lower respiratory tract in TB patients and healthy controls...
March 2018: Tuberculosis
Matthew Tien, Aretha Fiebig, Sean Crosson
Cells adapt to shifts in their environment by remodeling transcription. Measuring changes in transcription at the genome scale is now routine, but defining the functional significance of individual genes within large gene expression datasets remains a major challenge. We applied a network-based algorithm to interrogate publicly available gene expression data to predict genes that serve major functional roles in Caulobacter crescentus stress survival. This approach identified GsrN, a conserved small RNA that is directly activated by the general stress sigma factor, σT , and functions as a potent post-transcriptional regulator of survival across distinct conditions including osmotic and oxidative stress...
March 14, 2018: ELife
Asli Yildirim, Michael Feig
High-resolution three-dimensional models of Caulobacter crescentus nucleoid structures were generated via a multi-scale modeling protocol. Models were built as a plectonemically supercoiled circular DNA and by incorporating chromosome conformation capture based data to generate an ensemble of base pair resolution models consistent with the experimental data. Significant structural variability was found with different degrees of bending and twisting but with overall similar topologies and shapes that are consistent with C...
February 26, 2018: Nucleic Acids Research
Xiaoxian Wu, Diane L Haakonsen, Allen G Sanderlin, Yue J Liu, Liqiang Shen, Ningning Zhuang, Michael T Laub, Yu Zhang
Canonical bacterial transcription activators bind to non-transcribed promoter elements to increase transcription of their target genes. Here we report crystal structures of binary complexes comprising domains of Caulobacter crescentus GcrA, a noncanonical bacterial transcription factor, that support a novel mechanism for transcription activation through the preferential binding of methylated cis-regulatory elements and the promotion of open complex formation through an interaction with region 2 of the principal σ factor, σ70...
March 5, 2018: Nucleic Acids Research
Lisa Wasserstrom, Diogo Portugal-Nunes, Henrik Almqvist, Anders G Sandström, Gunnar Lidén, Marie F Gorwa-Grauslund
Engineering of the yeast Saccharomyces cerevisiae towards efficient D-xylose assimilation has been a major focus over the last decades since D-xylose is the second most abundant sugar in nature, and its conversion into products could significantly improve process economy in biomass-based processes. Up to now, two different metabolic routes have been introduced via genetic engineering, consisting of either the isomerization or the oxido-reduction of D-xylose to D-xylulose that is further connected to the pentose phosphate pathway and glycolysis...
March 5, 2018: AMB Express
Ryosuke Ikebe, Yuri Kuwabara, Taiki Chikada, Hironori Niki, Daisuke Shiomi
Rod shape of bacterial cells such as Escherichia coli is mainly regulated by a supramolecular complex called elongasome including MreB actin. Deletion of the mreB gene in rod-shaped bacterium E. coli results in round-shaped cells. RodZ was isolated as a determinant of rod shape in E. coli, Caulobacter crescentus and Bacillus subtilis and it has been shown to be an interaction partner and a regulator of assembly of MreB through its cytoplasmic domain. As opposed to functions of the N-terminal cytoplasmic domain of RodZ, functions of the C-terminal periplasmic domain including a disordered region are still unclear...
February 26, 2018: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
Ashraf S A El-Sayed, Asma Akbar, Irum Iqrar, Robina Ali, David Norman, Mary Brennan, Gul Shad Ali
Biological control is an eco-friendly strategy for mitigating and controlling plant diseases with negligible effects on human health and environment. Biocontrol agents are mostly isolated from field crops, and microbiomes associated with wild native plants is underexplored. The main objective of this study was to characterize the bacterial isolates associated with Smilax bona-nox L, a successful wild plant with invasive growth habits. Forty morphologically distinct bacterial isolates were recovered from S. bona-nox...
March 2018: Microbiological Research
Luca Rossoni, Reuben Carr, Scott Baxter, Roxann Cortis, Thomas Thorpe, Graham Eastham, Gill Stephens
Bio-production of fuels and chemicals from lignocellulosic C5 sugars usually requires the use of the pentose phosphate pathway (PPP) to produce pyruvate. Unfortunately, the oxidation of pyruvate to acetyl-coenzyme A results in the loss of 33 % of the carbon as CO2, to the detriment of sustainability and process economics. To improve atom efficiency, we engineered Escherichia coli to utilize d-xylose constitutively using the Weimberg pathway, to allow direct production of 2-oxoglutarate without CO2 loss. After confirming enzyme expression in vitro, the pathway expression was optimized in vivo using a combinatorial approach, by screening a range of constitutive promoters whilst systematically varying the gene order...
February 5, 2018: Microbiology
Christina Farr Zuend, John F Nomellini, John Smit, Marc S Horwitz
HSV-2 infection is a significant health problem and a major co-morbidity factor for HIV-1 acquisition, increasing risk of infection 2-4 fold. Condom based prevention strategies for HSV-2 and HIV-1 have not been effective at stopping the HIV-1 pandemic, indicating that alternative prevention strategies need to be investigated. We have previously developed an inexpensive HIV-1 specific microbicide that utilizes the S-layer mediated display capabilities of Caulobacter crescentus, and have shown that recombinant C...
February 12, 2018: Scientific Reports
Doreen Nguyen, Bert Ely
Bacteriophages remain an understudied component of bacterial communities. Therefore, our laboratory has initiated an effort to isolate large numbers of bacteriophages that infect Caulobacter crescentus to provide an estimate of the diversity of bacteriophages that infect this common environmental bacterium. The majority of the new isolates are phicbkviruses, a genus of giant viruses that appear to be Caulobacter specific. However, we have also isolated several Podoviruses with icosahedral heads and small tails...
February 8, 2018: Current Microbiology
Rhudith B Cabulong, Won-Keun Lee, Angelo B Bañares, Kristine Rose M Ramos, Grace M Nisola, Kris Niño G Valdehuesa, Wook-Jin Chung
Glycolic acid (GA) is an ⍺-hydroxy acid used in cosmetics, packaging, and medical industries due to its excellent properties, especially in its polymeric form. In this study, Escherichia coli was engineered to produce GA from D-xylose by linking the Dahms pathway, the glyoxylate bypass, and the partial reverse glyoxylate pathway (RGP). Initially, a GA-producing strain was constructed by disrupting the xylAB and glcD genes in the E. coli genome and overexpressing the xdh(Cc) from Caulobacter crescentus. This strain was further improved through modular optimization of the Dahms pathway and the glyoxylate bypass...
February 1, 2018: Applied Microbiology and Biotechnology
Michele Felletti, Deike J Omnus, Kristina Jonas
The decision to initiate DNA replication is a critical step in the cell cycle of all organisms. In nearly all bacteria, replication initiation requires the activity of the conserved replication initiation protein DnaA. Due to its central role in cell cycle progression, DnaA activity must be precisely regulated. This review summarizes the current state of DnaA regulation in the asymmetrically dividing α-proteobacterium Caulobacter crescentus, an important model for bacterial cell cycle studies. Mechanisms will be discussed that regulate DnaA activity and abundance under optimal conditions and in coordination with the asymmetric Caulobacter cell cycle...
January 31, 2018: Biochimica et Biophysica Acta
Camille V Goemans, François Beaufay, Khadija Wahni, Inge Van Molle, Joris Messens, Jean François Collet
Thioredoxins (Trxs) are antioxidant proteins that are conserved among all species. These proteins have been extensively studied and perform reducing reactions on a broad range of substrates. Here, we identified Caulobacter crescentus Trx1 (CCNA_03653; CcTrx1) as an oxidoreductase that is involved in the cell cycle progression of this model bacterium and is required to sustain life. Intriguingly, the abundance of CcTrx1 varies throughout the C. crescentus cell cycle: while the expression of CcTrx1 is induced in stalked cells, right before DNA replication initiation, CcTrx1 is actively degraded by the ClpXP protease in predivisional cells...
January 24, 2018: Journal of Biological Chemistry
Mohammad Mubinur Rahman, Martina Andberg, Anu Koivula, Juha Rouvinen, Nina Hakulinen
The Ilv/ED dehydratase protein family includes dihydroxy acid-, gluconate-, 6-phosphogluconate- and pentonate dehydratases. The members of this family are involved in various biosynthetic and carbohydrate metabolic pathways. Here, we describe the first crystal structure of D-xylonate dehydratase from Caulobacter crescentus (CcXyDHT) at 2.7 Å resolution and compare it with other available enzyme structures from the IlvD/EDD protein family. The quaternary structure of CcXyDHT is a tetramer, and each monomer is composed of two domains in which the N-terminal domain forms a binding site for a [2Fe-2S] cluster and a Mg2+ ion...
January 16, 2018: Scientific Reports
Jacques-Robert Christen, Edwin Edmond, Michel Drancourt
OBJECTIVE: Gemmata bacteria are fastidious, Gram-negative and aerobic. The only representatives are Gemmata obscuriglobus and Gemmata massiliana. These Planctomycetes appear to be a part of human digestive tract microbiome, and G. massiliana has been isolated from water. Further specific detection in the blood of two patients with febrile neutropenia suggests that Gemmata bacteremia may remain under-documented. The objective of this study was to develop an effective protocol to document Gemmata spp...
January 8, 2018: BMC Research Notes
Frederic D Schramm, Kristina Heinrich, Marietta Thüring, Jörg Bernhardt, Kristina Jonas
Hsp70 chaperones are well known for their important functions in maintaining protein homeostasis during thermal stress conditions. In many bacteria the Hsp70 homolog DnaK is also required for growth in the absence of stress. The molecular reasons underlying Hsp70 essentiality remain in most cases unclear. Here, we demonstrate that DnaK is essential in the α-proteobacterium Caulobacter crescentus due to its regulatory function in gene expression. Using a suppressor screen we identified mutations that allow growth in the absence of DnaK...
December 27, 2017: PLoS Genetics
Matthieu Bergé, Patrick H Viollier
Understanding how asymmetries in cellular constituents are achieved and how such positional information directs the construction of structures in a nonrandom fashion is a fundamental problem in cell biology. The recent identification of determinants that self-assemble into macromolecular complexes at the bacterial cell pole provides new insight into the underlying organizational principles in bacterial cells. Specifically, polarity studies in host-associated or free-living α-proteobacteria, a lineage of Gram-negative (diderm) bacteria, reveals that functional and cytological mono- and bipolarity is often conferred by the multivalent polar organizer PopZ, originally identified as a component of a polar chromosome anchor in the cell cycle model system Caulobacter crescentus...
November 29, 2017: Trends in Microbiology
Xin Wang, Nana Xu, Shewei Hu, Jianming Yang, Qian Gao, Sheng Xu, Kequan Chen, Pingkai Ouyang
Bio-based production of d-1,2,4-butanetriol (BT) from renewable substrates is increasingly attracting attention. Here, the BT biosynthetic pathway was constructed and optimized in Escherichia coli to produce BT from pure d-xylose or corncob hydrolysates. First, E. coli BL21(DE3) was identified as a more proper host for BT production through host screening. Then, BT pathway was systematically optimized with gene homolog screening strategy, mainly targeting three key steps from xylonic acid to BT catalyzed by d-xylonate dehydratase (XD), 2-keto acid decarboxylase (KDC) and aldehyde reductase (ALR)...
November 23, 2017: Bioresource Technology
Ngat T Tran, Clare E Stevenson, Nicolle F Som, Anyarat Thanapipatsiri, Adam S B Jalal, Tung B K Le
Proper chromosome segregation is essential in all living organisms. In Caulobacter crescentus, the ParA-ParB-parS system is required for proper chromosome segregation and cell viability. The bacterial centromere-like parS DNA locus is the first to be segregated following chromosome replication. parS is bound by ParB protein, which in turn interacts with ParA to partition the ParB-parS nucleoprotein complex to each daughter cell. Here, we investigated the genome-wide distribution of ParB on the Caulobacter chromosome using a combination of in vivo chromatin immunoprecipitation (ChIP-seq) and in vitro DNA affinity purification with deep sequencing (IDAP-seq)...
February 16, 2018: Nucleic Acids Research
Amrita Dubey, Richa Priyadarshini
Bacterial cell division is a complex process brought about by the coordinated action of multiple proteins. Separation of daughter cells during the final stages of division involves cleavage of new cell wall laid down at the division septum. In E. coli, this process is governed by the action of N-acetylmuramoyl-L-alanine amidases AmiA/B/C, which are regulated by their LytM activators EnvC and NlpD. While much is known about the regulation of septum cleavage in E. coli, the mechanism of daughter cell separation is not clear in Caulobacter crescentus, a dimorphic crescent-shaped bacterium...
November 22, 2017: Current Genetics
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