The Structure of the Carboxyltransferase Component of Acetyl-CoA Carboxylase Reveals a Zinc-Binding Motif Unique to the Bacterial Enzyme<sup>,</sup>

Bilder, P.W.; Lightle, Sandra; Bainbridge, G.R.; Ohren, Jeffrey F.; Finzel, B.C.; Sun, Fang; Holley, Susan; Al-Kassim, Loola; Spessard, Cindy; Melnick, Michael; Newcomer, Marcia E.; Waldrop, Grover L.

doi:10.1021/bi0520479

Cited by 78 publications

(83 citation statements)

References 37 publications

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“…For each CLPP and CLPR subunit (including the plastid-encoded ClpP1), changes that were inferred to have occurred in S. conica, S. paradoxa, or S. noctiflora from the ancestral Silene sequence were mapped onto the structure of an individual E. coli ClpP subunit (PDB accession 1YG6; Bewley et al 2006;Yu and Houry 2007). Likewise, changes in ACCase subunits were also mapped onto solved E. coli structures (PDB accessions 4HR7 and 2F9Y: Bilder et al 2006;Broussard et al 2013). Template structures from E. coli were used because no plant CLP or ACCase structures have been solved.…”

Section: Analysis Of Protein Structure and Position Of Substitutionsmentioning

confidence: 99%

Positive Selection in Rapidly Evolving Plastid–Nuclear Enzyme Complexes

et al. 2016

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Rates of sequence evolution in plastid genomes are generally low, but numerous angiosperm lineages exhibit accelerated evolutionary rates in similar subsets of plastid genes. These genes include clpP1 and accD, which encode components of the caseinolytic protease (CLP) and acetyl-coA carboxylase (ACCase) complexes, respectively. Whether these extreme and repeated accelerations in rates of plastid genome evolution result from adaptive change in proteins (i.e., positive selection) or simply a loss of functional constraint (i.e., relaxed purifying selection) is a source of ongoing controversy. To address this, we have taken advantage of the multiple independent accelerations that have occurred within the genus Silene (Caryophyllaceae) by examining phylogenetic and population genetic variation in the nuclear genes that encode subunits of the CLP and ACCase complexes. We found that, in species with accelerated plastid genome evolution, the nuclear-encoded subunits in the CLP and ACCase complexes are also evolving rapidly, especially those involved in direct physical interactions with plastid-encoded proteins. A massive excess of nonsynonymous substitutions between species relative to levels of intraspecific polymorphism indicated a history of strong positive selection (particularly in CLP genes). Interestingly, however, some species are likely undergoing loss of the native (heteromeric) plastid ACCase and putative functional replacement by a duplicated cytosolic (homomeric) ACCase. Overall, the patterns of molecular evolution in these plastidnuclear complexes are unusual for anciently conserved enzymes. They instead resemble cases of antagonistic coevolution between pathogens and host immune genes. We discuss a possible role of plastid-nuclear conflict as a novel cause of accelerated evolution.

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Section: Analysis Of Protein Structure and Position Of Substitutionsmentioning

confidence: 99%

Positive Selection in Rapidly Evolving Plastid–Nuclear Enzyme Complexes

et al. 2016

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“…Binding of BADC prevents binding of the essential BCCP subunit. The pool of BC/BCCP and BC/ BCCP/BADC subcomplexes then compete for interaction with the CT subcomplex (design based on crystal structure in E. coli; Bilder et al, 2006), leading to variable reductions in ACCase activity. While a transient association of the two ACCase half reactions is known, it is unclear whether BADC can displace BCCP from an assembled BC/BCCP subcomplex, hence the dashed arrows.…”

Section: Mass Spectrometry Sample Preparation and Analysismentioning

confidence: 99%

A Family of Negative Regulators Targets the Committed Step of de Novo Fatty Acid Biosynthesis

et al. 2016

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ORCID ID: 0000-0002-9686-9645 (V.L.)Acetyl-CoA carboxylase (ACCase) catalyzes the committed step of de novo fatty acid biosynthesis. In prokaryotes, green algae, and most plants, this enzyme is a heteromeric complex requiring four different subunits for activity. The plant complex is recalcitrant to conventional purification schemes and hence the structure and composition of the full assembly have been unclear. In vivo coimmunoprecipitation using subunit-specific antibodies identified a novel family of proteins in Arabidopsis thaliana annotated as biotin/lipoyl attachment domain containing (BADC) proteins. Results from yeast two-hybrid and coexpression in Escherichia coli confirmed that all three BADC isoforms interact with the two biotin carboxyl carrier protein (BCCP) isoforms of Arabidopsis ACCase. These proteins resemble BCCP subunits but are not biotinylated due to a mutated biotinylation motif. We demonstrate that BADC proteins significantly inhibit ACCase activity in both E. coli and Arabidopsis. Targeted gene silencing of BADC isoform 1 in Arabidopsis significantly increased seed oil content when normalized to either mass or individual seed. We conclude the BADC proteins are ancestral BCCPs that gained a new function as negative regulators of ACCase after initial loss of the biotinylation motif. A functional model is proposed.

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“…12(a)]. 67 Although the crystal structures were solved in the absence of bound substrates, site-directed mutagenesis and solution studies indicate that the a-subunits bind biotinylated-BCCP, whereas the b-subunits bind acetyl-CoA. The active sites lie at the interfaces between the a,b dimers [ Fig.…”

Section: E Coli and S Aureus Carboxyltransferasesmentioning

confidence: 99%

“…12(b)]. 67 The zinc finger is part of a saddle-like motif that is characterized by a patch of amino acids with a positive electrostatic surface potential. The rest of the protein has an overall negative electrostatic surface potential.…”

Section: E Coli and S Aureus Carboxyltransferasesmentioning

confidence: 99%

“…The rest of the protein has an overall negative electrostatic surface potential. 67 Zinc finger domains are commonly associated with proteins that bind nucleic acids, and, indeed, the E. coli and S. aureus carboxyltransferases were subsequently shown to bind DNA and RNA. 68,69 Using electrophoretic mobility shift assays, it was demonstrated that the E. coli carboxyltransferase specifically binds to the mRNA molecules encoding the a-and b-subunits, and this binding results in the inhibition of translation.…”

Section: E Coli and S Aureus Carboxyltransferasesmentioning

confidence: 99%

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The enzymes of biotin dependent CO₂ metabolism: What structures reveal about their reaction mechanisms

2012

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Biotin is the major cofactor involved in carbon dioxide metabolism. Indeed, biotindependent enzymes are ubiquitous in nature and are involved in a myriad of metabolic processes including fatty acid synthesis and gluconeogenesis. The cofactor, itself, is composed of a ureido ring, a tetrahydrothiophene ring, and a valeric acid side chain. It is the ureido ring that functions as the CO 2 carrier. A complete understanding of biotin-dependent enzymes is critically important for translational research in light of the fact that some of these enzymes serve as targets for antiobesity agents, antibiotics, and herbicides. Prior to 1990, however, there was a dearth of information regarding the molecular architectures of biotin-dependent enzymes. In recent years there has been an explosion in the number of three-dimensional structures reported for these proteins. Here we review our current understanding of the structures and functions of biotindependent enzymes. In addition, we provide a critical analysis of what these structures have and have not revealed about biotin-dependent catalysis.

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The Structure of the Carboxyltransferase Component of Acetyl-CoA Carboxylase Reveals a Zinc-Binding Motif Unique to the Bacterial Enzyme^,

Cited by 78 publications

References 37 publications

Positive Selection in Rapidly Evolving Plastid–Nuclear Enzyme Complexes

Positive Selection in Rapidly Evolving Plastid–Nuclear Enzyme Complexes

A Family of Negative Regulators Targets the Committed Step of de Novo Fatty Acid Biosynthesis

The enzymes of biotin dependent CO₂ metabolism: What structures reveal about their reaction mechanisms

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The Structure of the Carboxyltransferase Component of Acetyl-CoA Carboxylase Reveals a Zinc-Binding Motif Unique to the Bacterial Enzyme,

Cited by 78 publications

References 37 publications

Positive Selection in Rapidly Evolving Plastid–Nuclear Enzyme Complexes

Positive Selection in Rapidly Evolving Plastid–Nuclear Enzyme Complexes

A Family of Negative Regulators Targets the Committed Step of de Novo Fatty Acid Biosynthesis

The enzymes of biotin dependent CO2 metabolism: What structures reveal about their reaction mechanisms

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The Structure of the Carboxyltransferase Component of Acetyl-CoA Carboxylase Reveals a Zinc-Binding Motif Unique to the Bacterial Enzyme^,

The enzymes of biotin dependent CO₂ metabolism: What structures reveal about their reaction mechanisms