Artificial domain duplication replicates evolutionary history of ketol‐acid reductoisomerases

Cahn, John W.; Brinkmann‐Chen, Sabine; Buller, Andrew R.; Arnold, Frances H.

doi:10.1002/pro.2852

Cited by 6 publications

(8 citation statements)

References 62 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The E. coli IlvC also showed NADPH reduction. The E. coli IlvC protein has a higher K m value for acetolactate, 250±30 µM, as compared to IlvC of Mtb (K m for acetolactate=110±4 µM protein) [10,25]. The NADPH reduction confirmed that both Mtb-Ra and E. coli IlvCs were functional ketol-acid reductoisomerases and Mtb-Ra enzyme was able to complement the functionalities of E. coli enzyme.…”

Section: Discussionmentioning

confidence: 82%

“…The E. coli IlvC protein has a higher K m value for acetolactate, 250±30 µM, as compared to IlvC of Mtb ( K m for acetolactate=110±4 µM protein) [10, 25]. The NADPH reduction confirmed that both Mtb -Ra and E.…”

Section: Discussionmentioning

confidence: 99%

“…Studies in E. coli suggest that IlvC catalyzes both reactions, an isomerization consisting of an alkyl migration, followed by an NADPH-dependent reduction of 2-keto acid [24]. IlvCs have been defined as class I and class II based on their sequence length and oligomerization state, with class II having duplication at the C-terminal [25]. Sequence analysis of class I bacterial IlvCs suggest that the residues involved in active site formation are highly conserved [10].…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Biochemical and functional characterization of Mycobacterium tuberculosis ketol-acid reductoisomerase

et al. 2021

View full text Add to dashboard Cite

Branched-chain amino acids (BCAAs) are essential amino acids, but their biosynthetic pathway is absent in mammals. Ketol-acid reductoisomerase (IlvC) is a BCAA biosynthetic enzyme that is coded by Rv3001c in Mycobacterium tuberculosis H37Rv (Mtb-Rv) and MRA_3031 in M. tuberculosis H37Ra (Mtb-Ra). IlvCs are essential in Mtb-Rv as well as in Escherichia coli . Compared to wild-type and IlvC-complemented Mtb-Ra strains, IlvC knockdown strain showed reduced survival at low pH and under low pH+starvation stress conditions. Further, increased expression of IlvC was observed under low pH and starvation stress conditions. Confirmation of a role for IlvC in pH and starvation stress was achieved by developing E. coli BL21(DE3) IlvC knockout, which was defective for growth in M9 minimal medium, but growth could be rescued by isoleucine and valine supplementation. Growth was also restored by complementing with over-expressing constructs of Mtb-Ra and E. coli IlvCs. The E. coli knockout also had a survival deficit at pH=5.5 and 4.5 and was more susceptible to killing at pH=3.0. The biochemical characterization of Mtb-Ra and E. coli IlvCs confirmed that both have NADPH-dependent activity. In conclusion, this study demonstrates the functional complementation of E. coli IlvC by Mtb-Ra IlvC and also suggests that IlvC has a role in tolerance to low pH and starvation stress.

show abstract

Section: Discussionmentioning

confidence: 82%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Biochemical and functional characterization of Mycobacterium tuberculosis ketol-acid reductoisomerase

et al. 2021

View full text Add to dashboard Cite

show abstract

“…It is hypothesized that ancient domains arose by fusion of short peptide ancestors and that they are further diversified by fusion with other domains. Recently, researchers tested how duplicated domains formed through biological experiment (Cahn et al, 2016 ). They tested the possibility whether the class II ketol-acid reductoisomerase (KARI) have been produced from an ancestral class I KARI by duplication of the C-terminal domain and corresponding loss of obligate dimerization.…”

Section: Discussionmentioning

confidence: 99%

Origination, Expansion, Evolutionary Trajectory, and Expression Bias of AP2/ERF Superfamily in Brassica napus

Song

Wang

et al. 2016

Front. Plant Sci.

View full text Add to dashboard Cite

The AP2/ERF superfamily, one of the most important transcription factor families, plays crucial roles in response to biotic and abiotic stresses. So far, a comprehensive evolutionary inference of its origination and expansion has not been available. Here, we identified 515 AP2/ERF genes in B. napus, a neo-tetraploid forming ~7500 years ago, and found that 82.14% of them were duplicated in the tetraploidization. A prominent subgenome bias was revealed in gene expression, tissue-specific, and gene conversion. Moreover, a large-scale analysis across plants and alga suggested that this superfamily could have been originated from AP2 family, expanding to form other families (ERF, and RAV). This process was accompanied by duplicating and/or alternative deleting AP2 domain, intragenic domain sequence conversion, and/or by acquiring other domains, resulting in copy number variations, alternatively contributing to functional innovation. We found that significant positive selection occurred at certain critical nodes during the evolution of land plants, possibly responding to changing environment. In conclusion, the present research revealed origination, functional innovation, and evolutionary trajectory of the AP2/ERF superfamily, contributing to understanding their roles in plant stress tolerance.

show abstract

“…It is well known that recombination events can add or remove whole domains constituting long-scale mechanisms for domain architectural change 67 . In this context, tandem domain duplication provides a particular mechanism for modifying the oligomeric state of an enzyme without altering its function [68][69][70][71] . This occurred in the evolution of dimeric 6PGDHs, with the additional consideration that the duplication lead to the loss of two active sites in the oligomeric assembly.…”

Section: Discussionmentioning

confidence: 99%

Crystal structure of the 6-phosphogluconate dehydrogenase from Gluconobacter oxydans reveals tetrameric 6PGDHs as the crucial intermediate in the evolution of structure and cofactor preference in the 6PGDH family

et al. 2021

View full text Add to dashboard Cite

Background: The enzyme 6-phosphogluconate dehydrogenase (6PGDH) is the central enzyme of the oxidative pentose phosphate pathway. Members of the 6PGDH family belong to different classes: either homodimeric enzymes assembled from long-chain subunits or homotetrameric ones assembled from short-chain subunits. Dimeric 6PGDHs bear an internal duplication absent in tetrameric 6PGDHs and distant homologues of the β-hydroxyacid dehydrogenase (βHADH) superfamily. Methods: We use X-ray crystallography to determine the structure of the apo form of the 6PGDH from Gluconobacter oxydans (Go6PGDH). We carried out a structural and phylogenetic analysis of short and long-chain 6PGDHs. We put forward an evolutionary hypothesis explaining the differences seen in oligomeric state vs. dinucleotide preference of the 6PGDH family. We determined the cofactor preference of Go6PGDH at different 6-phosphogluconate concentrations, characterizing the wild-type enzyme and three-point mutants of residues in the cofactor binding site of Go6PGDH. Results: The structural comparison suggests that the 6PG binding site initially evolved by exchanging C-terminal α-helices between subunits. An internal duplication event changed the quaternary structure of the enzyme from a tetrameric to a dimeric arrangement. The phylogenetic analysis suggests that 6PGDHs have spread from Bacteria to Archaea and Eukarya on multiple occasions by lateral gene transfer. Sequence motifs consistent with NAD+- and NADP+-specificity are found in the β2-α2 loop of dimeric and tetrameric 6PGDHs. Site-directed mutagenesis of Go6PGDH inspired by this analysis fully reverses dinucleotide preference. One of the mutants we engineered has the highest efficiency and specificity for NAD+ so far described for a 6PGDH. Conclusions: The family 6PGDH comprises dimeric and tetrameric members whose active sites are conformed by a C-terminal α-helix contributed from adjacent subunits. Dimeric 6PGDHs have evolved from the duplication-fusion of the tetrameric C-terminal domain before independent transitions of cofactor specificity. Changes in the conserved β2-α2 loop are crucial to modulate the cofactor specificity in Go6PGDH.

show abstract

Artificial domain duplication replicates evolutionary history of ketol‐acid reductoisomerases

Cited by 6 publications

References 62 publications

Biochemical and functional characterization of Mycobacterium tuberculosis ketol-acid reductoisomerase

Biochemical and functional characterization of Mycobacterium tuberculosis ketol-acid reductoisomerase

Origination, Expansion, Evolutionary Trajectory, and Expression Bias of AP2/ERF Superfamily in Brassica napus

Crystal structure of the 6-phosphogluconate dehydrogenase from Gluconobacter oxydans reveals tetrameric 6PGDHs as the crucial intermediate in the evolution of structure and cofactor preference in the 6PGDH family

Contact Info

Product

Resources

About