The cAMP Receptor-Like Protein CLP Is a Novel c-di-GMP Receptor Linking Cell–Cell Signaling to Virulence Gene Expression in Xanthomonas campestris

Chin, Ko‐Hsin; Lee, Yen Chung; Tu, Zhi Le; Chen, Chih Hua; Tseng, Yi-Hsuan; Yang, Jinn-Moon; Ryan, Robert P.; McCarthy, Yvonne; Dow, J. Maxwell; Wang, Andrew H.J.; Chou, Shan‐Ho

doi:10.1016/j.jmb.2009.11.076

Cited by 178 publications

(189 citation statements)

References 63 publications

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“…Interestingly, an intrinsically active CRP homolog of the plant pathogen Xanthomonas campestris has an Asp residue at the corresponding position to G141 of E. coli CRP. A substitution of this Asp residue with the nonpolar residue Ala reduces the binding affinity to its promoter by ∼12-fold (36). In contrast to CRP G141D, the identified XylR variants not only enhance xylose utilization but also release CCR, leading to an efficient coutilization of glucose-xylose mixtures (Fig.…”

Section: Discussionmentioning

confidence: 96%

Experimental evolution reveals an effective avenue to release catabolite repression via mutations in XylR

Sievert

Nieves

Panyon

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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Microbial production of fuels and chemicals from lignocellulosic biomass provides promising biorenewable alternatives to the conventional petroleum-based products. However, heterogeneous sugar composition of lignocellulosic biomass hinders efficient microbial conversion due to carbon catabolite repression. The most abundant sugar monomers in lignocellulosic biomass materials are glucose and xylose. Although industrial Escherichia coli strains efficiently use glucose, their ability to use xylose is often repressed in the presence of glucose. Here we independently evolved three E. coli strains from the same ancestor to achieve high efficiency for xylose fermentation. Each evolved strain has a point mutation in a transcriptional activator for xylose catabolic operons, either CRP or XylR, and these mutations are demonstrated to enhance xylose fermentation by allelic replacements. Identified XylR variants (R121C and P363S) have a higher affinity to their DNA binding sites, leading to a xylose catabolic activation independent of catabolite repression control. Upon introducing these amino acid substitutions into the E. coli D-lactate producer TG114, 94% of a glucose–xylose mixture (50 g⋅L−1 each) was used in mineral salt media that led to a 50% increase in product titer after 96 h of fermentation. The two amino acid substitutions in XylR enhance xylose utilization and release glucose-induced repression in different E. coli hosts, including wild type, suggesting its potential wide application in industrial E. coli biocatalysts.

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Section: Discussionmentioning

confidence: 96%

Experimental evolution reveals an effective avenue to release catabolite repression via mutations in XylR

Sievert

Nieves

Panyon

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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“…To alter gene expression or protein activity in response to external or internal signals, c-di-GMP interacts with several proteins (1,2,(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17). In addition, two classes of RNAs have been reported that bind this second messenger, the c-di-GMP-I (class I) and c-di-GMP-II (class II) riboswitches (18,19).…”

mentioning

confidence: 99%

“…The affinity of these RNAs for their ligand is very high; class I riboswitches have a K d as tight as 10 pM (23) (1,2,(9)(10)(11)(12)(13)(14)(15)(16). Whereas a few bacteria contain examples of both classes, several species lacking a class I riboswitch use c-di-GMP for signaling and have exclusively a class II riboswitch (19).…”

mentioning

confidence: 99%

Structural basis of differential ligand recognition by two classes of bis-(3′-5′)-cyclic dimeric guanosine monophosphate-binding riboswitches

Smith

Shanahan

Moore

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

107

195

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The bis-(3′-5′)-cyclic dimeric guanosine monophosphate (c-di-GMP) signaling pathway regulates biofilm formation, virulence, and other processes in many bacterial species and is critical for their survival. Two classes of c-di-GMP-binding riboswitches have been discovered that bind this second messenger with high affinity and regulate diverse downstream genes, underscoring the importance of RNA receptors in this pathway. We have solved the structure of a c-di-GMP-II riboswitch, which reveals that the ligand is bound as part of a triplex formed with a pseudoknot. The structure also shows that the guanine bases of c-di-GMP are recognized through noncanonical pairings and that the phosphodiester backbone is not contacted by the RNA. Recognition is quite different from that observed in the c-di-GMP-I riboswitch, demonstrating that at least two independent solutions for RNA second messenger binding have evolved. We exploited these differences to design a c-di-GMP analog that selectively binds the c-di-GMP-II aptamer over the c-di-GMP-I RNA. There are several bacterial species that contain both types of riboswitches, and this approach holds promise as an important tool for targeting one riboswitch, and thus one gene, over another in a selective fashion.

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“…[23]. Clp is a homologue (45% amino acid sequence identity) of the model transcription factor CRP of E. coli.…”

Section: Discussionmentioning

confidence: 99%

Expressional Regulation of the Virulence Gene eglXoA Encoding Endoglucanase, Dependent on HrpXo and Cyclic AMP Receptor-Like Protein (Clp) in Xanthomonas oryzae pv. oryza

Temuujin¹,

Hw²

2017

J Plant Pathol Microbiol

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The cAMP Receptor-Like Protein CLP Is a Novel c-di-GMP Receptor Linking Cell–Cell Signaling to Virulence Gene Expression in Xanthomonas campestris

Cited by 178 publications

References 63 publications

Experimental evolution reveals an effective avenue to release catabolite repression via mutations in XylR

Experimental evolution reveals an effective avenue to release catabolite repression via mutations in XylR

Structural basis of differential ligand recognition by two classes of bis-(3′-5′)-cyclic dimeric guanosine monophosphate-binding riboswitches

Expressional Regulation of the Virulence Gene eglXoA Encoding Endoglucanase, Dependent on HrpXo and Cyclic AMP Receptor-Like Protein (Clp) in Xanthomonas oryzae pv. oryza

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