Diversification of Catalytic Activities and Ligand Interactions in the Protein Fold Shared by the Sugar Isomerases, eIF2B, DeoR Transcription Factors, Acyl-CoA Transferases and Methenyltetrahydrofolate Synthetase

Anantharaman, Vivek; Aravind, L.

doi:10.1016/j.jmb.2005.11.031

Cited by 22 publications

(29 citation statements)

References 71 publications

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“…For instance, E. coli DeoR, E. coli GlpR, E. coli UlaR, B. subtilis IolR, and Lactococcus lactis FruR control the metabolic systems for deoxyribonucleoside, glycerol-3-phosphate, L-ascorbate, myo-inositol, and fructose, and their effector molecules are deoxyribose-5-phosphate, glycerol-3-phosphate, L-ascorbate-6-phospate, 2-deoxy-5-keto-D-gluconate-6-phosphate, and fructose-1-phosphate, respectively (14)(15)(16)(17)(18). These DeoR members possess a conserved region near their C terminus, which is structurally related to E. coli D-ribose-5-phosphate isomerase, implying that this C-terminal region functions as the effector sensor (46). B. subtilis RhaR also possesses these conserved N-terminal and Cterminal regions, probably functioning as the DNA-binding domain and the domain for dimerization and effector binding, respectively.…”

Section: Discussionmentioning

confidence: 99%

Regulation of the rhaEWRBMA Operon Involved in l -Rhamnose Catabolism through Two Transcriptional Factors, RhaR and CcpA, in Bacillus subtilis

et al. 2016

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The Bacillus subtilis rhaEWRBMA (formerly yuxG-yulBCDE) operon consists of four genes encoding enzymes for L-rhamnose catabolism and the rhaR gene encoding a DeoR-type transcriptional regulator. DNase I footprinting analysis showed that the RhaR protein specifically binds to the regulatory region upstream of the rhaEW gene, in which two imperfect direct repeats are included. Gel retardation analysis revealed that the direct repeat farther upstream is essential for the high-affinity binding of RhaR and that the DNA binding of RhaR was effectively inhibited by L-rhamnulose-1-phosphate, an intermediate of L-rhamnose catabolism. Moreover, it was demonstrated that the CcpA/P-Ser-HPr complex, primarily governing the carbon catabolite control in B. subtilis, binds to the catabolite-responsive element, which overlaps the RhaR binding site. In vivo analysis of the rhaEW promoter-lacZ fusion in the background of ccpA deletion showed that the L-rhamnose-responsive induction of the rhaEW promoter was negated by the disruption of rhaA or rhaB but not rhaEW or rhaM, whereas rhaR disruption resulted in constitutive rhaEW promoter activity. These in vitro and in vivo results clearly indicate that RhaR represses the operon by binding to the operator site, which is detached by L-rhamnulose-1-phosphate formed from L-rhamnose through a sequence of isomerization by RhaA and phosphorylation by RhaB, leading to the derepression of the operon. In addition, the lacZ reporter analysis using the strains with or without the ccpA deletion under the background of rhaR disruption supported the involvement of CcpA in the carbon catabolite repression of the operon. IMPORTANCESince L-rhamnose is a component of various plant-derived compounds, it is a potential carbon source for plant-associating bacteria. Moreover, it is suggested that L-rhamnose catabolism plays a significant role in some bacteria-plant interactions, e.g., invasion of plant pathogens and nodulation of rhizobia. Despite the physiological importance of L-rhamnose catabolism for various bacterial species, the transcriptional regulation of the relevant genes has been poorly understood, except for the regulatory system of Escherichia coli. In this study, we show that, in Bacillus subtilis, one of the plant growth-promoting rhizobacteria, the rhaEWRBMA operon for L-rhamnose catabolism is controlled by RhaR and CcpA. This regulatory system can be another standard model for better understanding the regulatory mechanisms of L-rhamnose catabolism in other bacterial species. Bacillus subtilis is a soil-dwelling bacterium that has been extensively and closely studied as a Gram-positive model bacterium. B. subtilis species have often been isolated from the rhizosphere of various terrestrial plants; many of them have been shown to be plant growth-promoting rhizobacteria whose association with the plant roots enhances the adaptive potential of plants and increases their growth (1). Interestingly, B. subtilis is also a saprophytic bacterium that secretes various degrading enzymes, incl...

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Section: Discussionmentioning

confidence: 99%

Regulation of the rhaEWRBMA Operon Involved in l -Rhamnose Catabolism through Two Transcriptional Factors, RhaR and CcpA, in Bacillus subtilis

et al. 2016

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“…Their effectors are usually phosphorylated intermediates in the metabolic pathways that they control, e.g., glycerol-3-phosphate (GlpR), L-ascorbate-6-phosphate (UlaR), fructose-1-phosphate (FruR), 2-deoxy-5-keto-D-gluconate-6-phosphate (IolR), and deoxyribose-5-phosphate (DeoR) (5,14,19,25,43). These DeoR members possess a conserved region near their C terminus that is structurally related to E. coli D-ribose-5-phosphate isomerase, implying that this C-terminal region functions as the effector sensor (1). Distinct from these members, the C-terminal region of YcnK does not retain such a conserved sugar-phosphate recognition region but resembles the C-terminal regions of the NosL proteins, which are considered to act as copper chaperones involved in the metallo-center assembly of nitrous oxide reductase.…”

Section: Discussionmentioning

confidence: 99%

Direct and Indirect Regulation of the ycnKJI Operon Involved in Copper Uptake through Two Transcriptional Repressors, YcnK and CsoR, in Bacillus subtilis

et al. 2012

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Northern blot and primer extension analyses revealed that the ycnKJI operon and the ycnL gene of Bacillus subtilis are transcribed from adjacent promoters that are divergently oriented. The ycnK and ycnJ genes encode a DeoR-type transcriptional regulator and a membrane protein involved in copper uptake, respectively. DNA binding experiments showed that the YcnK protein specifically binds to the ycnK-ycnL intergenic region, including a 16-bp direct repeat that is essential for the high binding affinity of YcnK, and that a copper-specific chelator significantly inhibits YcnK's DNA binding. lacZ reporter analysis showed that the ycnK promoter is induced by copper limitation or ycnK disruption. These results are consistent with YcnK functioning as a copper-responsive repressor that derepresses ycnKJI expression under copper limitation. On the other hand, the ycnL promoter was hardly induced by copper limitation, but ycnK disruption resulted in a slight induction of the ycnL promoter, suggesting that YcnK also represses ycnL weakly. Moreover, while the CsoR protein did not bind to the ycnK-ycnL intergenic region, lacZ reporter analysis demonstrated that csoR disruption induces the ycnK promoter only in the presence of intact ycnK and copZA genes. Since the copZA operon is involved in copper export and repressed by CsoR, it appears that the constitutive copZA expression brought by csoR disruption causes intracellular copper depletion, which releases the repression of the ycnKJI operon by YcnK.

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“…42 Amongst the Rossmannoid folds two major divisions can be recognized: (1) the nucleotide binding domains with a nucleotide binding loop between strand 1 and the helix after it. This group includes many large monophyletic assemblages of proteins, namely the classic Rossmann NAD/FAD-dependent dehydrogenases, 43 Sir2-like deacetylases, 44 the S-AdoMet-binding methyltransferases, [45][46][47] the GTPase FtsZ, 48 the ISO-COT fold 49 and the HUP superclass (class I tRNA synthetases, HIGH nucleotidyltransferases, USPA, photolyase and electron transport flavoprotein). 42 Most members of this division are characterized by specific signatures, often glycine-rich, in their nucleotide-binding loops.…”

Section: Relationship Of the Had Superfamily To Other Rossmannoid Foldsmentioning

confidence: 99%

Evolutionary Genomics of the HAD Superfamily: Understanding the Structural Adaptations and Catalytic Diversity in a Superfamily of Phosphoesterases and Allied Enzymes

Burroughs¹,

Allen²,

Dunaway‐Mariano³

et al. 2006

Journal of Molecular Biology

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387

520

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The HAD (haloacid dehalogenase) superfamily includes phosphoesterases, ATPases, phosphonatases, dehalogenases, and sugar phosphomutases acting on a remarkably diverse set of substrates. The availability of numerous crystal structures of representatives belonging to diverse branches of the HAD superfamily provides us with a unique opportunity to reconstruct their evolutionary history and uncover the principal determinants that led to their diversification of structure and function. To this end we present a comprehensive analysis of the HAD superfamily that identifies their unique structural features and provides a detailed classification of the entire superfamily. We show that at the highest level the HAD superfamily is unified with several other superfamilies, namely the DHH, receiver (CheY-like), von Willebrand A, TOPRIM, classical histone deacetylases and PIN/FLAP nuclease domains, all of which contain a specific form of the Rossmannoid fold. These Rossmannoid folds are distinguished from others by the presence of equivalently placed acidic catalytic residues, including one at the end of the first core β-strand of the central sheet. The HAD domain is distinguished from these related Rossmannoid folds by two key structural signatures, a "squiggle" (a single helical turn) and a "flap" (a beta hairpin motif) located immediately downstream of the first β-strand of their core Rossmanoid fold. The squiggle and the flap motifs are predicted to provide the necessary mobility to these enzymes for them to alternate between the "open" and "closed" conformations. In addition, most members of the HAD superfamily contains inserts, termed caps, occurring at either of two positions in the core Rossmannoid fold. We show that the cap modules have been independently inserted into these two stereotypic positions on multiple occasions in evolution and display extensive evolutionary diversification independent of the core catalytic domain. The first group of caps, the C1 caps, is directly inserted into the flap motif and regulates access of reactants to the active site. The second group, the C2 caps, forms a roof over the active site, and access to their internal cavities might be in part regulated by the movement of the flap. The diversification of the cap module was a major factor in the exploration of a vast substrate space in the course of the evolution of this superfamily. We show that the HAD superfamily contains 33 major families distributed across the three superkingdoms of life. Analysis of the phyletic patterns suggests that at least five distinct HAD proteins are traceable to the last universal common ancestor (LUCA) of all extant organisms. While these prototypes diverged prior to the emergence Abbreviations used: HAD, haloacid dehalogenase; PNKP, polynucleotide kinase phosphatase; KDO 8-P, deoxy-Dmannose-octulosonate 8-phosphate; CTD, carboxyl-terminal domain; PNKP, polynucleotide kinase phosphatase; LUCA, last universal common ancestor.E-mail address of the corresponding author: aravind@ncbi.nlm.nih.gov of the LUCA, t...

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Diversification of Catalytic Activities and Ligand Interactions in the Protein Fold Shared by the Sugar Isomerases, eIF2B, DeoR Transcription Factors, Acyl-CoA Transferases and Methenyltetrahydrofolate Synthetase

Cited by 22 publications

References 71 publications

Regulation of the rhaEWRBMA Operon Involved in l -Rhamnose Catabolism through Two Transcriptional Factors, RhaR and CcpA, in Bacillus subtilis

Regulation of the rhaEWRBMA Operon Involved in l -Rhamnose Catabolism through Two Transcriptional Factors, RhaR and CcpA, in Bacillus subtilis

Direct and Indirect Regulation of the ycnKJI Operon Involved in Copper Uptake through Two Transcriptional Repressors, YcnK and CsoR, in Bacillus subtilis

Evolutionary Genomics of the HAD Superfamily: Understanding the Structural Adaptations and Catalytic Diversity in a Superfamily of Phosphoesterases and Allied Enzymes

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