scholarly journals Carbohydrate Utilization Patterns for the Extremely Thermophilic Bacterium Caldicellulosiruptor saccharolyticus Reveal Broad Growth Substrate Preferences

2009 ◽  
Vol 75 (24) ◽  
pp. 7718-7724 ◽  
Author(s):  
Amy L. VanFossen ◽  
Marcel R. A. Verhaart ◽  
Servé M. W. Kengen ◽  
Robert M. Kelly
Keyword(s):  
Transcriptional Response ◽  
Thermophilic Bacterium ◽  
Open Reading Frames ◽  
Transport Systems ◽  
Response Analysis ◽  
Growth Substrate ◽  
Phosphotransferase System ◽  
Carbohydrate Utilization ◽  
Caldicellulosiruptor Saccharolyticus ◽  
Substrate Preferences

ABSTRACT Coutilization of hexoses and pentoses derived from lignocellulose is an attractive trait in microorganisms considered for consolidated biomass processing to biofuels. This issue was examined for the H2-producing, extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus growing on individual monosaccharides (arabinose, fructose, galactose, glucose, mannose, and xylose), mixtures of these sugars, as well as on xylan and xylogluco-oligosacchrides. C. saccharolyticus grew at approximately the same rate (t d, ∼95 min) and to the same final cell density (1 × 108 to 3 × 108 cells/ml) on all sugars and sugar mixtures tested. In the monosaccharide mixture, although simultaneous consumption of all monosaccharides was observed, not all were utilized to the same extent (fructose > xylose/arabinose > mannose/glucose/galactose). Transcriptome contrasts for monosaccharide growth revealed minimal changes in some cases (e.g., 32 open reading frames [ORFs] changed ≥2-fold for glucose versus galactose), while substantial changes occurred for cases involving mannose (e.g., 353 ORFs changed ≥2-fold for glucose versus mannose). Evidence for catabolite repression was not noted for either growth on multisugar mixtures or the corresponding transcriptomes. Based on the whole-genome transcriptional response analysis and comparative genomics, carbohydrate specificities for transport systems could be proposed for most of the 24 putative carbohydrate ATP-binding cassette transporters and single phosphotransferase system identified in C. saccharolyticus. Although most transporter genes responded to individual monosaccharides and polysaccharides, the genes Csac_0692 to Csac_0694 were upregulated only in the monosaccharide mixture. The results presented here affirm the broad growth substrate preferences of C. saccharolyticus on carbohydrates representative of lignocellulosic biomass and suggest that this bacterium holds promise for biofuel applications.

scholarly journals Whole-Genome Analysis of Transporters in the Plant Pathogen Xylella fastidiosa

2002 ◽  
Vol 66 (2) ◽  
pp. 272-299 ◽  
Author(s):  
Joao Meidanis ◽  
Marilia D. V. Braga ◽  
Sergio Verjovski-Almeida
Keyword(s):  
Xylella Fastidiosa ◽  
Open Reading Frames ◽  
Transport Systems ◽  
Phosphotransferase System ◽  
Whole Genome Analysis ◽  
Plant Parasite ◽  
Intracellular Parasites ◽  
P Type ◽  
Import System ◽  
Reading Frames

SUMMARY The transport systems of the first completely sequenced genome of a plant parasite, Xylella fastidiosa, were analyzed. In all, 209 proteins were classified here as constitutive members of transport families; thus, we have identified 69 new transporters in addition to the 140 previously annotated. The analysis lead to several hints on potential ways of controlling the disease it causes on citrus trees. An ADP:ATP translocator, previously found in intracellular parasites only, was found in X. fastidiosa. A P-type ATPase is missing—among the 24 completely sequenced eubacteria to date, only three (including X. fastidiosa) do not have a P-type ATPase, and they are all parasites transmitted by insect vectors. An incomplete phosphotransferase system (PTS) was found, without the permease subunits—we conjecture either that they are among the hypothetical proteins or that the PTS plays a solely metabolic regulatory role. We propose that the Ttg2 ABC system might be an import system eventually involved in glutamate import rather than a toluene exporter, as previously annotated. X. fastidiosa exhibits fewer proteins with ≥4 α-helical transmembrane spanners than any other completely sequenced prokaryote to date. X. fastidiosa has only 2.7% of all open reading frames identifiable as major transporters, which puts it as the eubacterium having the lowest percentage of open reading frames involved in transport, closer to two archaea, Methanococcus jannaschii (2.4%) and Methanobacterium thermoautotrophicum (2.4%).

scholarly journals Hyperthermophilic Thermotoga Species Differ with Respect to Specific Carbohydrate Transporters and Glycoside Hydrolases

2012 ◽  
Vol 78 (6) ◽  
pp. 1978-1986 ◽  
Author(s):  
Andrew D. Frock ◽  
Steven R. Gray ◽  
Robert M. Kelly
Keyword(s):  
Glucose Transporter ◽  
Open Reading Frames ◽  
The Other ◽  
Glycoside Hydrolases ◽  
Phosphotransferase System ◽  
Separate Species ◽  
Carbohydrate Utilization ◽  
Content Type ◽  
Sugar Transporters ◽  
Distinguishing Features

ABSTRACTFour hyperthermophilic members of the bacterial genusThermotoga(T. maritima,T. neapolitana,T. petrophila, andThermotogasp. strain RQ2) share a core genome of 1,470 open reading frames (ORFs), or about 75% of their genomes. Nonetheless, each species exhibited certain distinguishing features during growth on simple and complex carbohydrates that correlated with genomic inventories of specific ABC sugar transporters and glycoside hydrolases. These differences were consistent with transcriptomic analysis based on a multispecies cDNA microarray. Growth on a mixture of six pentoses and hexoses showed no significant utilization of galactose or mannose by any of the four species.T. maritimaandT. neapolitanaexhibited similar monosaccharide utilization profiles, with a strong preference for glucose and xylose over fructose and arabinose.Thermotogasp. strain RQ2 also used glucose and xylose, but was the only species to utilize fructose to any extent, consistent with a phosphotransferase system (PTS) specific for this sugar encoded in its genome.T. petrophilaused glucose to a significantly lesser extent than the other species. In fact, the XylR regulon was triggered by growth on glucose forT. petrophila, which was attributed to the absence of a glucose transporter (XylE2F2K2), otherwise present in the otherThermotogaspecies. This suggested thatT. petrophilaacquires glucose through the XylE1F1K1 transporter, which primarily serves to transport xylose in the other threeThermotogaspecies. The results here show that subtle differences exist among the hyperthermophilicThermotogaleswith respect to carbohydrate utilization, which supports their designation as separate species.

scholarly journals Cross-utilization of β-galactosides and cellobiose in Geobacillus stearothermophilus

2020 ◽  
Vol 295 (31) ◽  
pp. 10766-10780
Author(s):  
Smadar Shulami ◽  
Arie Zehavi ◽  
Valery Belakhov ◽  
Rachel Salama ◽  
Shifra Lansky ◽  
...  
Keyword(s):  
Transport System ◽  
Linear Growth ◽  
Growth Curves ◽  
Thermophilic Bacterium ◽  
Transport Systems ◽  
Geobacillus Stearothermophilus ◽  
Phosphotransferase System ◽  
Sensing System ◽  
Galactose Transport ◽  
Logarithmic Growth

Strains of the Gram-positive, thermophilic bacterium Geobacillus stearothermophilus possess elaborate systems for the utilization of hemicellulolytic polysaccharides, including xylan, arabinan, and galactan. These systems have been studied extensively in strains T-1 and T-6, representing microbial models for the utilization of soil polysaccharides, and many of their components have been characterized both biochemically and structurally. Here, we characterized routes by which G. stearothermophilus utilizes mono- and disaccharides such as galactose, cellobiose, lactose, and galactosyl-glycerol. The G. stearothermophilus genome encodes a phosphoenolpyruvate carbohydrate phosphotransferase system (PTS) for cellobiose. We found that the cellobiose-PTS system is induced by cellobiose and characterized the corresponding GH1 6-phospho-β-glucosidase, Cel1A. The bacterium also possesses two transport systems for galactose, a galactose-PTS system and an ABC galactose transporter. The ABC galactose transport system is regulated by a three-component sensing system. We observed that both systems, the sensor and the transporter, utilize galactose-binding proteins that also bind glucose with the same affinity. We hypothesize that this allows the cell to control the flux of galactose into the cell in the presence of glucose. Unexpectedly, we discovered that G. stearothermophilus T-1 can also utilize lactose and galactosyl-glycerol via the cellobiose-PTS system together with a bifunctional 6-phospho-β-gal/glucosidase, Gan1D. Growth curves of strain T-1 growing in the presence of cellobiose, with either lactose or galactosyl-glycerol, revealed initially logarithmic growth on cellobiose and then linear growth supported by the additional sugars. We conclude that Gan1D allows the cell to utilize residual galactose-containing disaccharides, taking advantage of the promiscuity of the cellobiose-PTS system.

scholarly journals Insights into the Mode of Action of Chitosan as an Antibacterial Compound

2008 ◽  
Vol 74 (12) ◽  
pp. 3764-3773 ◽  
Author(s):  
Dina Raafat ◽  
Kristine von Bargen ◽  
Albert Haas ◽  
Hans-Georg Sahl
Keyword(s):  
Antimicrobial Activity ◽  
Cell Wall ◽  
Cell Membrane ◽  
Mode Of Action ◽  
Membrane Lipids ◽  
Expression Profiles ◽  
Transcriptional Response ◽  
Response Analysis ◽  
Sequence Of Events ◽  
Wide Range

ABSTRACT Chitosan is a polysaccharide biopolymer that combines a unique set of versatile physicochemical and biological characteristics which allow for a wide range of applications. Although its antimicrobial activity is well documented, its mode of action has hitherto remained only vaguely defined. In this work we investigated the antimicrobial mode of action of chitosan using a combination of approaches, including in vitro assays, killing kinetics, cellular leakage measurements, membrane potential estimations, and electron microscopy, in addition to transcriptional response analysis. Chitosan, whose antimicrobial activity was influenced by several factors, exhibited a dose-dependent growth-inhibitory effect. A simultaneous permeabilization of the cell membrane to small cellular components, coupled to a significant membrane depolarization, was detected. A concomitant interference with cell wall biosynthesis was not observed. Chitosan treatment of Staphylococcus simulans 22 cells did not give rise to cell wall lysis; the cell membrane also remained intact. Analysis of transcriptional response data revealed that chitosan treatment leads to multiple changes in the expression profiles of Staphylococcus aureus SG511 genes involved in the regulation of stress and autolysis, as well as genes associated with energy metabolism. Finally, a possible mechanism for chitosan's activity is postulated. Although we contend that there might not be a single classical target that would explain chitosan's antimicrobial action, we speculate that binding of chitosan to teichoic acids, coupled with a potential extraction of membrane lipids (predominantly lipoteichoic acid) results in a sequence of events, ultimately leading to bacterial death.

scholarly journals Analysis of Predicted Carbohydrate Transport Systems Encoded by Bifidobacterium bifidum PRL2010

2012 ◽  
Vol 78 (14) ◽  
pp. 5002-5012 ◽  
Author(s):  
Francesca Turroni ◽  
Francesco Strati ◽  
Elena Foroni ◽  
Fausta Serafini ◽  
Sabrina Duranti ◽  
...  
Keyword(s):  
Bifidobacterium Bifidum ◽  
Transport Systems ◽  
Carbohydrate Utilization ◽  
Content Type ◽  
Carbohydrate Transport ◽  
Small Set ◽  
Transcriptome Analyses ◽  
Growth Experiments

ABSTRACTTheBifidobacterium bifidumPRL2010 genome encodes a relatively small set of predicted carbohydrate transporters. Growth experiments and transcriptome analyses ofB. bifidumPRL2010 revealed that carbohydrate utilization in this microorganism appears to be restricted to a relatively low number of carbohydrates.

Inactivation of the Streptococcus mutans fxpC Gene Confers Resistance to Xylitol, a Caries-preventive Natural Carbohydrate Sweetener

2002 ◽  
Vol 81 (6) ◽  
pp. 380-386 ◽  
Author(s):  
H. Benchabane ◽  
L.-A. Lortie ◽  
N.D. Buckley ◽  
L. Trahan ◽  
M. Frenette
Keyword(s):  
Streptococcus Mutans ◽  
Northern Blot Analysis ◽  
Regulatory Protein ◽  
Open Reading Frames ◽  
Phosphotransferase System ◽  
Chain Reactions ◽  
Polymerase Chain Reactions ◽  
Resistant Strains ◽  
Polymerase Chain ◽  
Reading Frames

Xylitol is transported by Streptococcus mutans via a constitutive phosphoenolpyruvate:fructose phosphotransferase system (PTS) composed of a IIABC protein. Spontaneous xylitol-resistant strains are depleted in constitutive fructose-PTS activity, exhibit additional phenotypes, and are associated with the caries-preventive properties of xylitol. Polymerase chain-reactions and chromosome walking were used to clone the fxp operon that codes for the constitutive fructose/xylitol-PTS. The operon contained three open reading frames: fxpA, which coded for a putative regulatory protein of the deoxyribose repressor (DeoR) family, fxpB, which coded for a 1-phosphofructokinase, and fxpC, which coded for a IIABC protein of the fructose-PTS family. Northern blot analysis revealed that these genes were co-transcribed into a 4.4-kb mRNA even in the absence of fructose. Inactivation of the fxpC gene conferred resistance to xylitol, confirming its function. The fxp operon is also present in the genomes of other xylitol-sensitive streptococci, which could explain their sensitivity to xylitol.

scholarly journals Functional-Genomics-Based Identification and Characterization of Open Reading Frames Encoding α-Glucoside-Processing Enzymes in the Hyperthermophilic Archaeon Pyrococcus furiosus

2007 ◽  
Vol 74 (4) ◽  
pp. 1281-1283 ◽  
Author(s):  
Donald A. Comfort ◽  
Chung-Jung Chou ◽  
Shannon B. Conners ◽  
Amy L. VanFossen ◽  
Robert M. Kelly
Keyword(s):  
Glycoside Hydrolase ◽  
Bioinformatics Analysis ◽  
Pyrococcus Furiosus ◽  
Transcriptional Response ◽  
Open Reading Frames ◽  
Processing Enzymes ◽  
Response Information ◽  
Identification And Characterization ◽  
Reading Frames

ABSTRACT Bioinformatics analysis and transcriptional response information for Pyrococcus furiosus grown on α-glucans led to the identification of a novel isomaltase (PF0132) representing a new glycoside hydrolase (GH) family, a novel GH57 β-amylase (PF0870), and an extracellular starch-binding protein (1,141 amino acids; PF1109-PF1110), in addition to several other putative α-glucan-processing enzymes.

Characterization of a recombinant β-glucosidase from the thermophilic bacterium Caldicellulosiruptor saccharolyticus

2009 ◽  
Vol 108 (1) ◽  
pp. 36-40 ◽  
Author(s):  
Mi-Ri Hong ◽  
Yeong-Su Kim ◽  
Chang-Su Park ◽  
Jung-Kul Lee ◽  
Yeong-Suk Kim ◽  
...  
Keyword(s):  
Thermophilic Bacterium ◽  
Caldicellulosiruptor Saccharolyticus

scholarly journals Genetic Composition of the Bacillus subtilis SOS System

2005 ◽  
Vol 187 (22) ◽  
pp. 7655-7666 ◽  
Author(s):  
Nora Au ◽  
Elke Kuester-Schoeck ◽  
Veena Mandava ◽  
Laura E. Bothwell ◽  
Susan P. Canny ◽  
...  
Keyword(s):  
Dna Damage ◽  
Bacillus Subtilis ◽  
Binding Sites ◽  
Consensus Sequence ◽  
Transcriptional Response ◽  
Open Reading Frames ◽  
Mobility Shift ◽  
E Coli ◽  
Recombination Protein ◽  
Lexa Binding

ABSTRACT The SOS response in bacteria includes a global transcriptional response to DNA damage. DNA damage is sensed by the highly conserved recombination protein RecA, which facilitates inactivation of the transcriptional repressor LexA. Inactivation of LexA causes induction (derepression) of genes of the LexA regulon, many of which are involved in DNA repair and survival after DNA damage. To identify potential RecA-LexA-regulated genes in Bacillus subtilis, we searched the genome for putative LexA binding sites within 300 bp upstream of the start codons of all annotated open reading frames. We found 62 genes that could be regulated by putative LexA binding sites. Using mobility shift assays, we found that LexA binds specifically to DNA in the regulatory regions of 54 of these genes, which are organized in 34 putative operons. Using DNA microarray analyses, we found that 33 of the genes with LexA binding sites exhibit RecA-dependent induction by both mitomycin C and UV radiation. Among these 33 SOS genes, there are 22 distinct LexA binding sites preceding 18 putative operons. Alignment of the distinct LexA binding sites reveals an expanded consensus sequence for the B. subtilis operator: 5′-CGAACATATGTTCG-3′. Although the number of genes controlled by RecA and LexA in B. subtilis is similar to that of Escherichia coli, only eight B. subtilis RecA-dependent SOS genes have homologous counterparts in E. coli.

Spiroplasma cells utilize carbohydrates via the phosphoenolpyruvate-dependent sugar phosphotransferase system

1991 ◽  
Vol 37 (6) ◽  
pp. 477-479 ◽  
Author(s):  
Mark Tarshis
Keyword(s):  
Cell Suspension ◽  
Key Words ◽  
Direct Measurement ◽  
Phosphotransferase System ◽  
Sulfhydryl Reagents ◽  
Carbohydrate Utilization ◽  
Sugar Utilization ◽  
Washed Cell ◽  
Phosphate Donor ◽  
Washed Cell Suspension

Ten Spiroplasma species tested were found capable of fermenting glucose, mannose, fructose, and sucrose, but not ribose, maltose, 2-deoxyglucose, xylose, sorbitol, glactose, lactose, and arabinose. Sugar utilization was measured by a direct measurement of the changes in pH of a washed cell suspension upon the addition of the various sugars. Sulfhydryl reagents, uncouplers, and glycolysis inhibitors prevented the sugar-induced pH shifts. The spiroplasmas were capable of phosporylating α-methylgucoside in a reaction that required phosphoenolypyruvate, but not ATP, as a phosphate donor, suggesting that Spiroplasma species possess a phosphoenolpyruvate-dependent sugar phosphotransferase system. Key words: Spiroplasma, carbohydrate utilization, pH changes, phosphenolpyruvate-dependent sugar phosphotransferase system.

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