scholarly journals Molecular mechanism of environmental d-xylose perception by a XylFII-LytS complex in bacteria

2017 ◽  
Vol 114 (31) ◽  
pp. 8235-8240 ◽  
Author(s):  
Jianxu Li ◽  
Chengyuan Wang ◽  
Gaohua Yang ◽  
Zhe Sun ◽  
Hui Guo ◽  
...  
Keyword(s):  
Conformational Change ◽  
Molecular Mechanism ◽  
Plant Biomass ◽  
Response Regulator ◽  
Specific Binding ◽  
Xylose Utilization ◽  
Chemical Production ◽  
Xylose Metabolism ◽  
Signal Perception ◽  
Large Conformational Change

d-xylose, the main building block of plant biomass, is a pentose sugar that can be used by bacteria as a carbon source for bio-based fuel and chemical production through fermentation. In bacteria, the first step for d-xylose metabolism is signal perception at the membrane. We previously identified a three-component system in Firmicutes bacteria comprising a membrane-associated sensor protein (XylFII), a transmembrane histidine kinase (LytS) for periplasmic d-xylose sensing, and a cytoplasmic response regulator (YesN) that activates the transcription of the target ABC transporter xylFGH genes to promote the uptake of d-xylose. The molecular mechanism underlying signal perception and integration of these processes remains elusive, however. Here we purified the N-terminal periplasmic domain of LytS (LytSN) in a complex with XylFII and determined the conformational structures of the complex in its d-xylose–free and d-xylose–bound forms. LytSN contains a four-helix bundle, and XylFII contains two Rossmann fold-like globular domains with a xylose-binding cleft between them. In the absence of d-xylose, LytSN and XylFII formed a heterodimer. Specific binding of d-xylose to the cleft of XylFII induced a large conformational change that closed the cleft and brought the globular domains closer together. This conformational change led to the formation of an active XylFII-LytSN heterotetramer. Mutations at the d-xylose binding site and the heterotetramer interface diminished heterotetramer formation and impaired the d-xylose–sensing function of XylFII-LytS. Based on these data, we propose a working model of XylFII-LytS that provides a molecular basis for d-xylose utilization and metabolic modification in bacteria.

scholarly journals A microtubule-dynein tethering complex regulates the axonemal inner dynein f (I1)

2018 ◽  
Vol 29 (9) ◽  
pp. 1060-1074 ◽  
Author(s):  
Tomohiro Kubo ◽  
Yuqing Hou ◽  
Deborah A. Cochran ◽  
George B. Witman ◽  
Toshiyuki Oda
Keyword(s):  
Conformational Change ◽  
Molecular Mechanism ◽  
Wild Type ◽  
Sliding Direction ◽  
Large Conformational Change ◽  
Dynein Arms ◽  
Biochemical Analyses

Motility of cilia/flagella is generated by a coordinated activity of thousands of dyneins. Inner dynein arms (IDAs) are particularly important for the formation of ciliary/flagellar waveforms, but the molecular mechanism of IDA regulation is poorly understood. Here we show using cryoelectron tomography and biochemical analyses of Chlamydomonas flagella that a conserved protein FAP44 forms a complex that tethers IDA f (I1 dynein) head domains to the A-tubule of the axonemal outer doublet microtubule. In wild-type flagella, IDA f showed little nucleotide-dependent movement except for a tilt in the f β head perpendicular to the microtubule-sliding direction. In the absence of the tether complex, however, addition of ATP and vanadate caused a large conformational change in the IDA f head domains, suggesting that the movement of IDA f is mechanically restricted by the tether complex. Motility defects in flagella missing the tether demonstrates the importance of the IDA f-tether interaction in the regulation of ciliary/flagellar beating.

scholarly journals Reciprocal Regulation of l-Arabinose and d-Xylose Metabolism in Escherichia coli

2015 ◽  
Vol 198 (3) ◽  
pp. 386-393 ◽  
Author(s):  
Santosh Koirala ◽  
Xiaoyi Wang ◽  
Christopher V. Rao
Keyword(s):  
Escherichia Coli ◽  
Plant Biomass ◽  
Single Cells ◽  
Xylose Utilization ◽  
Xylose Metabolism ◽  
Reciprocal Regulation ◽  
Content Type ◽  
E Coli ◽  
Metabolic Genes ◽  
Mixed Populations

ABSTRACTGlucose is known to inhibit the transport and metabolism of many sugars inEscherichia coli. This mechanism leads to its preferential consumption. Far less is known about the preferential utilization of nonglucose sugars inE. coli. Two exceptions arel-arabinose andd-xylose. Previous studies have shown thatl-arabinose inhibitsd-xylose metabolism inEscherichia coli. This repression results froml-arabinose-bound AraC binding to the promoter of thed-xylose metabolic genes and inhibiting their expression. This mechanism, however, has not been explored in single cells. Both thel-arabinose andd-xylose utilization systems are known to exhibit a bimodal induction response to their cognate sugar, where mixed populations of cells either expressing the metabolic genes or not are observed at intermediate sugar concentrations. This suggests thatl-arabinose can only inhibitd-xylose metabolism inl-arabinose-induced cells. To understand how cross talk between these systems affects their response, we investigatedE. coliduring growth on mixtures ofl-arabinose andd-xylose at single-cell resolution. Our results showed that mixed, multimodal populations ofl-arabinose- andd-xylose-induced cells occurred at intermediate sugar concentrations. We also found thatd-xylose inhibited the expression of thel-arabinose metabolic genes and that this repression was due to XylR. These results demonstrate that a strict hierarchy does not exist betweenl-arabinose andd-xylose as previously thought. The results may also aid in the design ofE. colistrains capable of simultaneous sugar consumption.IMPORTANCEGlucose,d-xylose, andl-arabinose are the most abundant sugars in plant biomass. Developing efficient fermentation processes that convert these sugars into chemicals and fuels will require strains capable of coutilizing these sugars. Glucose has long been known to repress the expression of thel-arabinose andd-xylose metabolic genes inEscherichia coli. Recent studies found thatl-arabinose also represses the expression of thed-xylose metabolic genes. In the present study, we found thatd-xylose also represses the expression of thel-arabinose metabolic genes, leading to mixed populations of cells capable of utilizingl-arabinose andd-xylose. These results further our understanding of mixed-sugar utilization and may aid in strain design.

scholarly journals Insights into genome recoding from the mechanism of a classic +1-frameshifting tRNA

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Howard Gamper ◽  
Haixing Li ◽  
Isao Masuda ◽  
D. Miklos Robkis ◽  
Thomas Christian ◽  
...  
Keyword(s):  
Amino Acids ◽  
Conformational Change ◽  
Molecular Mechanism ◽  
Late Stage ◽  
Anticodon Loop ◽  
Pairing Mechanism ◽  
Extra Nucleotide ◽  
In Cells

AbstractWhile genome recoding using quadruplet codons to incorporate non-proteinogenic amino acids is attractive for biotechnology and bioengineering purposes, the mechanism through which such codons are translated is poorly understood. Here we investigate translation of quadruplet codons by a +1-frameshifting tRNA, SufB2, that contains an extra nucleotide in its anticodon loop. Natural post-transcriptional modification of SufB2 in cells prevents it from frameshifting using a quadruplet-pairing mechanism such that it preferentially employs a triplet-slippage mechanism. We show that SufB2 uses triplet anticodon-codon pairing in the 0-frame to initially decode the quadruplet codon, but subsequently shifts to the +1-frame during tRNA-mRNA translocation. SufB2 frameshifting involves perturbation of an essential ribosome conformational change that facilitates tRNA-mRNA movements at a late stage of the translocation reaction. Our results provide a molecular mechanism for SufB2-induced +1 frameshifting and suggest that engineering of a specific ribosome conformational change can improve the efficiency of genome recoding.

scholarly journals The Ability of a Novel Strain Scheffersomyces (Syn. Candida) shehatae Isolated from Rotten Wood to Produce Arabitol

2017 ◽  
Vol 66 (3) ◽  
pp. 335-343 ◽  
Author(s):  
Monika Kordowska-Wiater ◽  
Adam Kuzdraliński ◽  
Tomasz Czernecki ◽  
Zdzisław Targoński ◽  
Magdalena Frąc ◽  
...  
Keyword(s):  
Energy Density ◽  
Plant Biomass ◽  
Optimum Conditions ◽  
Candida Shehatae ◽  
Chemical Production ◽  
Biotechnological Production ◽  
Rotten Wood ◽  
Optimization Study ◽  
Pharmaceutical Industries ◽  
Interesting Alternative

Arabitol is a polyalcohol which has about 70% of the sweetness of sucrose and an energy density of 0.2 kcal/g. Similarly to xylitol, it can be used in the food and pharmaceutical industries as a natural sweetener, a texturing agent, a dental caries reducer, and a humectant. Biotechnological production of arabitol from sugars represents an interesting alternative to chemical production. The yeast Scheffersomyces shehatae strain 20BM-3 isolated from rotten wood was screened for its ability to produce arabitol from L-arabinose, glucose, and xylose. This isolate, cultured at 28°C and 150 rpm, secreted 4.03 ± 0.00 to 7.97 ± 0.67 g/l of arabitol from 17–30 g/l of L-arabinose assimilated from a medium containing 20–80 g/l of this pentose with yields of 0.24 ± 0.00 to 0.36 ± 0.02 g/g. An optimization study demonstrated that pH 4.0, 32°C, and a shaking frequency of 150 rpm were the optimum conditions for arabitol production by the investigated strain. Under these conditions, strain 20BM-3 produced 6.2 ± 0.17 g/l of arabitol from 17.5 g/l of arabinose after 4 days with a yield of 0.35 ± 0.01 g/g. This strain also produced arabitol from glucose, giving much lower yields, but did not produce it from xylose. The new strain can be successfully used for arabitol production from abundantly available sugars found in plant biomass.

Molecular mechanism of the calcium-induced conformational change in the spectrin EF-hands.

1995 ◽  
Vol 14 (20) ◽  
pp. 4922-4931 ◽  
Author(s):  
G. Travé ◽  
P. J. Lacombe ◽  
M. Pfuhl ◽  
M. Saraste ◽  
A. Pastore
Keyword(s):  
Conformational Change ◽  
Molecular Mechanism ◽  
Ef Hands

scholarly journals Light and heat control over secondary structure and amyloid-like fiber formation in an overcrowded-alkene-modified Trp zipper

2015 ◽  
Vol 6 (12) ◽  
pp. 7311-7318 ◽  
Author(s):  
Claudia Poloni ◽  
Marc C. A. Stuart ◽  
Pieter van der Meulen ◽  
Wiktor Szymanski ◽  
Ben L. Feringa
Keyword(s):  
Secondary Structure ◽  
Conformational Change ◽  
Fiber Formation ◽  
Major Influence ◽  
Heat Control ◽  
Large Conformational Change

The use of an overcrowded alkene photoswitch to control a model β-hairpin peptide is described. The light-induced, large conformational change has major influence on the secondary structure and the aggregation of the peptide, permitting the triggered formation of amyloid-like fibrils.

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