Evolution of allosteric regulation in chorismate mutases from early plants

2017 ◽  
Vol 474 (22) ◽  
pp. 3705-3717 ◽  
Author(s):  
Kourtney Kroll ◽  
Cynthia K. Holland ◽  
Courtney M. Starks ◽  
Joseph M. Jez
Keyword(s):  
Physcomitrella Patens ◽  
Sequence Similarity ◽  
Allosteric Regulation ◽  
Aromatic Amino Acids ◽  
Negative Regulator ◽  
Chorismate Mutase ◽  
Basal Angiosperm ◽  
Allosteric Effector ◽  
Selaginella Moellendorffii ◽  
Tyrosine Biosynthesis

Plants, fungi, and bacteria synthesize the aromatic amino acids: l-phenylalanine, l-tyrosine, and l-tryptophan. Chorismate mutase catalyzes the branch point reaction of phenylalanine and tyrosine biosynthesis to generate prephenate. In Arabidopsis thaliana, there are two plastid-localized chorismate mutases that are allosterically regulated (AtCM1 and AtCM3) and one cytosolic isoform (AtCM2) that is unregulated. Previous analysis of plant chorismate mutases suggested that the enzymes from early plants (i.e. bryophytes/moss, lycophytes, and basal angiosperms) formed a clade distinct from the isoforms found in flowering plants; however, no biochemical information on these enzymes is available. To understand the evolution of allosteric regulation in plant chorismate mutases, we analyzed a basal lineage of plant enzymes homologous to AtCM1 based on sequence similarity. The chorismate mutases from the moss/bryophyte Physcomitrella patens (PpCM1 and PpCM2), the lycophyte Selaginella moellendorffii (SmCM), and the basal angiosperm Amborella trichopoda (AmtCM1 and AmtCM2) were characterized biochemically. Tryptophan was a positive effector for each of the five enzymes examined. Histidine was a weak positive effector for PpCM1 and AmtCM1. Neither tyrosine nor phenylalanine altered the activity of SmCM; however, tyrosine was a negative regulator of the other four enzymes. Phenylalanine down-regulates both moss enzymes and AmtCM2. The 2.0 Å X-ray crystal structure of PpCM1 in complex with the tryptophan identified the allosteric effector site and reveals structural differences between the R- (more active) and T-state (less active) forms of plant chorismate mutases. Molecular insight into the basal plant chorismate mutases guides our understanding of the evolution of allosteric regulation in these enzymes.

scholarly journals The Two Chorismate Mutases from both Mycobacterium tuberculosis and Mycobacterium smegmatis: Biochemical Analysis and Limited Regulation of Promoter Activity by Aromatic Amino Acids

2007 ◽  
Vol 190 (1) ◽  
pp. 122-134 ◽  
Author(s):  
Cristopher Z. Schneider ◽  
Tanya Parish ◽  
Luiz A. Basso ◽  
Diógenes S. Santos
Keyword(s):  
Amino Acids ◽  
Mycobacterium Tuberculosis ◽  
Mycobacterium Smegmatis ◽  
Sequence Similarity ◽  
Aromatic Amino Acids ◽  
Open Reading Frames ◽  
Chorismate Mutase ◽  
Structural Class ◽  
Promising Target ◽  
Translational Start

ABSTRACT Chorismate mutase (CM) catalyzes the rearrangement of chorismate to prephenate in the biosynthetic pathway that forms phenylalanine and tyrosine in bacteria, fungi, plants, and apicomplexan parasites. Since this enzyme is absent from mammals, it represents a promising target for the development of new antimycobacterial drugs, which are needed to combat Mycobacterium tuberculosis, the causative agent of tuberculosis. Until recently, two putative open reading frames (ORFs), Rv0948c and Rv1885c, showing low sequence similarity to CMs have been described as “conserved hypothetical proteins” in the M. tuberculosis genome. However, we and others demonstrated that these ORFs are in fact monofunctional CMs of the AroQ structural class and that they are differentially localized in the mycobacterial cell. Since homologues to the M. tuberculosis enzymes are also present in Mycobacterium smegmatis, we cloned the coding sequences corresponding to ORFs MSMEG5513 and MSMEG2114 from the latter. The CM activities of both ORFs was determined, as well as their translational start sites. In addition, we analyzed the promoter activities of three M. tuberculosis loci related to phenylalanine and tyrosine biosynthesis under a variety of conditions using M. smegmatis as a surrogate host. Our results indicate that the aroQ (Rv0948c), *aroQ (Rv1885c), and fbpB (Rv1886c) genes from M. tuberculosis are constitutively expressed or subjected to minor regulation by aromatic amino acids levels, especially tryptophan.

scholarly journals Diversified amino acid-mediated allosteric regulation of phosphoglycerate dehydrogenase for serine biosynthesis in land plants

2021 ◽  
Author(s):  
Eiji Okamura ◽  
Kinuka Ohtaka ◽  
Ryuichi Nishihama ◽  
Kai Uchida ◽  
Ayuko Kuwahara ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Physcomitrella Patens ◽  
Allosteric Regulation ◽  
Site Directed Mutagenesis ◽  
Land Plants ◽  
Basal Angiosperm ◽  
Marchantia Polymorpha ◽  
Phosphoglycerate Dehydrogenase ◽  
Serine Biosynthesis

The phosphorylated pathway of serine biosynthesis is initiated with 3-phosphoglycerate dehydrogenase (PGDH). The liverwort Marchantia polymorpha possesses an amino acid-sensitive MpPGDH which is inhibited by L-serine and activated by five proteinogenic amino acids, while the eudicot Arabidopsis thaliana has amino acid-sensitive AtPGDH1 and AtPGDH3 as well as amino acid-insensitive AtPGDH2. In this study, we analyzed PGDH isozymes of the representative land plants: the monocot Oryza sativa (OsPGDH1‒3), basal angiosperm Amborella trichopoda (AmtriPGDH1‒2), and moss Physcomitrium (Physcomitrella) patens (PpPGDH1‒4). We demonstrated that OsPGDH1, AmtriPGDH1, PpPGDH1, and PpPGDH3 were amino acid-sensitive, whereas OsPGDH2, OsPGDH3, AmtriPGDH2, PpPGDH2 and PpPGDH4 were either sensitive to only some of the six effector amino acids or insensitive to all effectors. This indicates that PGDH sensitivity to effectors has been diversified among isozymes and that the land plant species examined, except for M. polymorpha, possess different isozyme types in terms of regulation. Phylogenetic analysis suggested that the different sensitivities convergently evolved in the bryophyte and angiosperm lineages. Site-directed mutagenesis of AtPGDH1 revealed that Asp538 and Asn556 residues in the ACT domain are involved in allosteric regulation by the effectors. These findings provide insight into the evolution of PGDH isozymes, highlighting the functional diversification of allosteric regulation in land plants.

The Expression of Sel1L and Tan-1 in Normal and Neoplastic Cells

2000 ◽  
Vol 15 (1) ◽  
pp. 26-32 ◽  
Author(s):  
M. Cattaneo ◽  
R. Orlandi ◽  
C. Ronchini ◽  
P. Granelli ◽  
G. Malferrari ◽  
...  
Keyword(s):  
Cell Function ◽  
Sequence Similarity ◽  
Expression Patterns ◽  
Negative Regulator ◽  
Chromosomal Mapping ◽  
Normal Adult ◽  
Neoplastic Cells ◽  
C Elegans ◽  
Pancreatic Cancers ◽  
Almost All

We have previously reported on the isolation and chromosomal mapping of a novel human gene (SEL1L), which shows sequence similarity to sel-1, an extragenic suppressor of C. elegans. sel-1 functions as a negative regulator of lin-12 activity, the latter being implicated in the control of diverse cellular differentiation events. In the present study we compare the expression patterns of SEL1L and TAN-1, the human ortholog of lin-12 in normal and neoplastic cells. We found that, whereas both genes are expressed in fetal tissues at similar levels, they are differentially expressed in normal adult and neoplastic cells. In normal adult cells SEL1L is generally present at very low levels; only in the cells of the pancreas does it show maximum expression. By contrast, SEL1L is generally well represented in most neoplastic cells but not in those of pancreatic and gastric carcinomas, where transcription is either downregulated or completely repressed. TAN-1 on the other hand is well represented in almost all normal and neoplastic cells, with very few exceptions. Our observations suggest that SEL1L is presumably implicated in pancreatic and gastric carcinogenesis and that, along with TAN-1, it is very important for normal cell function. Alterations in the expression of SEL1L may be used as a prognostic marker for gastric and pancreatic cancers.

scholarly journals Molecular cloning of RBCS genes in Selaginella and the evolution of the rbcS gene family

2015 ◽  
Vol 67 (2) ◽  
pp. 373-383
Author(s):  
Bo Wang ◽  
Su Yingjuan ◽  
Ting Wang
Keyword(s):  
Gene Family ◽  
Physcomitrella Patens ◽  
Higher Plants ◽  
Genome Wide ◽  
A Genome ◽  
Rbcs Gene ◽  
Rbcs Genes ◽  
Selaginella Moellendorffii ◽  
Insight Into ◽  
Major Domain

Rubisco small subunits (RBCS) are encoded by a nuclear rbcS multigene family in higher plants and green algae. However, owing to the lack of rbcS sequences in lycophytes, the characteristics of rbcS genes in lycophytes is unclear. Recently, the complete genome sequence of the lycophyte Selaginella moellendorffii provided the first insight into the rbcS gene family in lycophytes. To understand further the characteristics of rbcS genes in other Selaginella, the full length of rbcS genes (rbcS1 and rbcS2) from two other Selaginella species were isolated. Both rbcS1 and rbcS2 genes shared more than 97% identity among three Selaginella species. RBCS proteins from Selaginella contained the Pfam RBCS domain F00101, which was a major domain of other plant RBCS proteins. To explore the evolution of the rbcS gene family across Selaginella and other plants, we identified and performed comparative analysis of the rbcS gene family among 16 model plants based on a genome-wide analysis. The results showed that (i) two rbcS genes were obtained in Selaginella, which is the second fewest number of rbcS genes among the 16 representative plants; (ii) an expansion of rbcS genes occurred in the moss Physcomitrella patens; (iii) only RBCS proteins from angiosperms contained the Pfam PF12338 domains, and (iv) a pattern of concerted evolution existed in the rbcS gene family. Our study provides new insights into the evolution of the rbcS gene family in Selaginella and other plants.

Phenylalanine and Tyrosine Biosynthesis in Sporeforming Members of the Order Actinomycetales

1987 ◽  
Vol 42 (4) ◽  
pp. 387-393 ◽  
Author(s):  
Hilda-K. Hund ◽  
Brigitte Keller ◽  
Franz Lingens
Keyword(s):  
Anion Exchange ◽  
Deae Cellulose ◽  
Anion Exchange Chromatography ◽  
Exchange Chromatography ◽  
Chorismate Mutase ◽  
Biosynthetic Enzymes ◽  
Prephenate Dehydratase ◽  
Prephenate Dehydrogenase ◽  
Arogenate Dehydrogenase ◽  
Tyrosine Biosynthesis

Abstract The enzymes of the terminal steps of phenylalanine and tyrosine biosynthesis, chorismate mutase, prephenate dehydratase, arogenate dehydratase, prephenate dehydrogenase and aroge­ nate dehydrogenase were studied in 13 sporeforming members of the order Actinomycetales. In these organisms tyrosine is synthesized exclusively via arogenate, phenylalanine, however, via phenylpyruvate. The regulation pattern of the corresponding enzymes was determined: No feed­ back inhibition of arogenate dehydrogenase by L-phenylalanine and ʟ-tyrosine was observed. Chorismate mutase was found to be inhibited in all organisms by ʟ-tyrosine and in most organisms by ʟ-tryptophan. ʟ-Phenylalanine was shown to inhibit prephenate dehydratase in the majority of bacteria tested and ʟ-tyrosine activated this enzyme in most cases. The elution profiles for the phenylalanine and tyrosine biosynthetic enzymes were studied in three members of the order Actinomycetales by anion exchange chromatography on DEAE-cellulose.

scholarly journals Sst2, a negative regulator of pheromone signaling in the yeast Saccharomyces cerevisiae: expression, localization, and genetic interaction and physical association with Gpa1 (the G-protein alpha subunit).

1996 ◽  
Vol 16 (9) ◽  
pp. 5194-5209 ◽  
Author(s):  
H G Dohlman ◽  
J Song ◽  
D Ma ◽  
W E Courchesne ◽  
J Thorner
Keyword(s):  
G Protein ◽  
Gene Product ◽  
Genetic Interaction ◽  
Sequence Similarity ◽  
Negative Regulator ◽  
Rgs Proteins ◽  
Pheromone Response ◽  
Yeast Saccharomyces Cerevisiae ◽  
Terminal Domain ◽  
Cell Extracts

Sst2 is the prototype for the newly recognized RGS (for regulators of G-protein signaling) family. Cells lacking the pheromone-inducible SST2 gene product fail to resume growth after exposure to pheromone. Conversely, overproduction of Sst2 markedly enhanced the rate of recovery from pheromone-induced arrest in the long-term halo bioassay and detectably dampened signaling in a short-term assay of pheromone response (phosphorylation of Ste4, Gbeta subunit). When the GPA1 gene product (Galpha subunit) is absent, the pheromone response pathway is constitutively active and, consequently, growth ceases. Despite sustained induction of Sst2 (observed with specific anti-Sst2 antibodies), gpa1delta mutants remain growth arrested, indicating that the action of Sst2 requires the presence of Gpa1. The N-terminal domain (residues 3 to 307) of Sst2 (698 residues) has sequence similarity to the catalytic regions of bovine GTPase-activating protein and human neurofibromatosis tumor suppressor protein; segments in the C-terminal domain of Sst2 (between residues 417 and 685) are homologous to other RGS proteins. Both the N- and C-terminal domains were required for Sst2 function in vivo. Consistent with a role for Sst2 in binding to and affecting the activity of Gpa1, the majority of Sst2 was membrane associated and colocalized with Gpa1 at the plasma membrane, as judged by sucrose density gradient fractionation. Moreover, from cell extracts, Sst2 could be isolated in a complex with Gpa1 (expressed as a glutathione S-transferase fusion); this association withstood the detergent and salt conditions required for extraction of these proteins from cell membranes. Also, SST2+ cells expressing a GTPase-defective GPA1 mutant displayed an increased sensitivity to pheromone, whereas sst2 cells did not. These results demonstrate that Sst2 and Gpa1 interact physically and suggest that Sst2 is a direct negative regulator of Gpa1.

An engineered chorismate mutase with allosteric regulation

2003 ◽  
Vol 11 (14) ◽  
pp. 3109-3114 ◽  
Author(s):  
Sheng Zhang ◽  
David B Wilson ◽  
Bruce Ganem
Keyword(s):  
Allosteric Regulation ◽  
Chorismate Mutase

scholarly journals Biochemical and Structural Characterization of the Secreted Chorismate Mutase (Rv1885c) from Mycobacterium tuberculosis H37Rv: an *AroQ Enzyme Not Regulated by the Aromatic Amino Acids

2006 ◽  
Vol 188 (24) ◽  
pp. 8638-8648 ◽  
Author(s):  
Sook-Kyung Kim ◽  
Sathyavelu K. Reddy ◽  
Bryant C. Nelson ◽  
Gregory B. Vasquez ◽  
Andrew Davis ◽  
...  
Keyword(s):  
Amino Acids ◽  
Mycobacterium Tuberculosis ◽  
Active Site ◽  
Signal Sequence ◽  
Aromatic Amino Acids ◽  
Helical Structure ◽  
Data Bank ◽  
Chorismate Mutase ◽  
Site Directed Mutagenesis ◽  
Single Chain

ABSTRACT The gene Rv1885c from the genome of Mycobacterium tuberculosis H37Rv encodes a monofunctional and secreted chorismate mutase (*MtCM) with a 33-amino-acid cleavable signal sequence; hence, it belongs to the *AroQ class of chorismate mutases. Consistent with the heterologously expressed *MtCM having periplasmic destination in Escherichia coli and the absence of a discrete periplasmic compartment in M. tuberculosis, we show here that *MtCM secretes into the culture filtrate of M. tuberculosis. *MtCM functions as a homodimer and exhibits a dimeric state of the protein at a concentration as low as 5 nM. *MtCM exhibits simple Michaelis-Menten kinetics with a Km of 0.5 ± 0.05 mM and a k cat of 60 s−1 per active site (at 37°C and pH 7.5). The crystal structure of *MtCM has been determined at 1.7 Å resolution (Protein Data Bank identifier 2F6L). The protein has an all alpha-helical structure, and the active site is formed within a single chain without any contribution from the second chain in the dimer. Analysis of the structure shows a novel fold topology for the protein with a topologically rearranged helix containing Arg134. We provide evidence by site-directed mutagenesis that the residues Arg49, Lys60, Arg72, Thr105, Glu109, and Arg134 constitute the catalytic site; the numbering of the residues includes the signal sequence. Our investigation on the effect of phenylalanine, tyrosine, and tryptophan on *MtCM shows that *MtCM is not regulated by the aromatic amino acids. Consistent with this observation, the X-ray structure of *MtCM does not have an allosteric regulatory site.

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