Modelling the evolution of the archeal tryptophan synthase

Merkl, Rainer

doi:10.1186/1471-2148-7-59

Cited by 29 publications

(25 citation statements)

References 58 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Present investigation has been correlated with the many studies made by various scientists, [17][18][19][20][21][22][23][24][25][26][27][28]. The studies supports the findings of the present study specially the sequence and structure analyzed against the standards taken (Pfu beta 2 subunit with Stm beta subunit of tryptophan synthase) for sequence analysis and structure prediction.…”

Section: Discussionsupporting

confidence: 75%

Comparative Study of Tryptophan Synthase Beta Chainbetween Pyrococcus furiosus (Archaea) and Salmonella typhimurium (Proteobacteria)

Bisht¹,

Behera²,

Panda³

2011

IJBBB

View full text Add to dashboard Cite

Abstract-The present investigation deals with comparative study of beta chain of the enzyme tryptophan synthase from Salmonella typhimurium and Pyrococcus furiosus. The study yielded few significant results that the sequence of beta 2 subunit (PF1706) from Pfu is closely related to the beta chain of Salmonella typhimurium in comparison to the beta 1. The phylogenetics of these two strains indicates that the beta 2 subunit plays a vital role in tryptophan synthesis in Pyrococcus furiosus. In the present investigation Salmonella typhimurium was used as a reference organism for comparative genomics of tryptophan synthase beta chain amongst a group of organisms 13 archaea and 41 proteobacteria respectively. The study reveals that most of the sequences of archaea are distantly related and was observed that there are certain sequences like pfu PF1706 which are closer to Stm that is a proteobacteria.

show abstract

Section: Discussionsupporting

confidence: 75%

Comparative Study of Tryptophan Synthase Beta Chainbetween Pyrococcus furiosus (Archaea) and Salmonella typhimurium (Proteobacteria)

Bisht¹,

Behera²,

Panda³

2011

IJBBB

View full text Add to dashboard Cite

show abstract

“…We selected three phylogenetically diverse TrpBs [10] to serve as the basis for new standalone catalysts: the hyperthermostable enzymes from Archaeoglobus fulgidus (AfTrpB, 72% sequence identity to PfTrpB) and Thermotoga maritima (TmTrpB, 64% identity), and the mesophilic enzyme from Escherichia coli (EcTrpB, 57% identity). [11] We were especially interested in TmTrpB because its wild-type k cat is already four times that of PfTrpB.…”

Section: Introductionmentioning

confidence: 99%

A Panel of TrpB Biocatalysts Derived from Tryptophan Synthase through the Transfer of Mutations that Mimic Allosteric Activation

et al. 2016

View full text Add to dashboard Cite

Naturally occurring enzyme homologs often display highly divergent activity with non-natural substrates. Exploiting this diversity with enzymes engineered for new or altered function, however, is laborious because the engineering must be replicated for each homolog. We demonstrate that a small set of mutations of the tryptophan synthase β-subunit (TrpB) from Pyrococcus furiosus, which mimic the activation afforded by binding of the α-subunit, has a similar activating effect in TrpB homologs with as little as 57% sequence identity. Kinetic and spectroscopic analyses indicate that the mutations function through the same mechanism, mimicry of α-subunit binding. From this collection of stand-alone enzymes, we identified a new catalyst that displays a remarkably broad activity profile in the synthesis of 5-substituted tryptophans, a biologically important class of compounds. This investigation demonstrates how allosteric activation can be recapitulated throughout a protein family to efficiently explore natural sequence diversity for desirable biocatalytic transformations. TOC imageThe tryptophan synthase enzyme complex is active toward a number of indole analogs. The β-subunit (TrpB) performs the synthetically useful reaction, but requires the α-subunit to be fully active. We have transferred mutations from a re-activated TrpB variant from Pyrococcus furiosus into homologous TrpBs to generate a panel of stand-alone TrpB catalysts, one of which is especially useful for making 5-substituted tryptophans, an important biological motif.

show abstract

“…However, this does not exclude the possibility that the loop and bulge in Group 2 59SLs interact with their respective TRAP molecules. It is important to note that tryptophan biosynthesis genes are considered poor markers for characterizing an organism's overall evolutionary pathway (Brown and Doolittle 1997;Merkl 2007), and the phylogenetic relationships discussed here do not necessarily reflect genomic evolution (Gutierrez-Preciado et al 2007).…”

Section: Implications For In Vivo Functionmentioning

confidence: 99%

TRAP-5′ stem–loop interaction increases the efficiency of transcription termination in the Bacillus subtilis trpEDCFBA operon leader region

McGraw¹,

Bevilacqua²,

Babitzke³

2007

RNA

View full text Add to dashboard Cite

TRAP regulates expression of the Bacillus subtilis trpEDCFBA operon by a transcription attenuation mechanism in which tryptophan-activated TRAP binds to 11 (G/U)AG repeats in the nascent trp leader transcript. Bound TRAP blocks formation of an antiterminator structure and allows formation of an overlapping intrinsic terminator upstream of the trp operon structural genes. A 59 stem-loop (59SL) structure located upstream of the triplet repeat region also interacts with TRAP. TRAP-59SL RNA interaction participates in the transcription attenuation mechanism by preferentially increasing the affinity of TRAP for the nascent trp leader transcript during the early stages of transcription, when only a few triplet repeats have been synthesized. Footprinting assays indicated that the 59SL contacts TRAP through two discrete groups of single-stranded nucleotides that lie in the hairpin loop and in an internal loop. Filter binding and in vivo expression assays of 59SL mutants established that G7, A8, and A9 from the internal loop, and A19 and G20 from the hairpin loop are critical for proper 59SL function. These nucleotides are conserved among certain other 59SL-containing organisms. Single-round transcription results indicated that the 59SL increases the termination efficiency when transcription is fast; however, the influence of the 59SL was lost when transcription was slowed by reducing the ribonucleoside triphosphate concentration. Since there is a limited amount of time for TRAP to bind to the nascent transcript and promote termination, our data suggest that the contribution of TRAP-59SL interaction increases the rate of TRAP binding, which, in turn, increases the efficiency of transcription termination.

show abstract

Modelling the evolution of the archeal tryptophan synthase

Cited by 29 publications

References 58 publications

Comparative Study of Tryptophan Synthase Beta Chainbetween Pyrococcus furiosus (Archaea) and Salmonella typhimurium (Proteobacteria)

Comparative Study of Tryptophan Synthase Beta Chainbetween Pyrococcus furiosus (Archaea) and Salmonella typhimurium (Proteobacteria)

A Panel of TrpB Biocatalysts Derived from Tryptophan Synthase through the Transfer of Mutations that Mimic Allosteric Activation

TRAP-5′ stem–loop interaction increases the efficiency of transcription termination in the Bacillus subtilis trpEDCFBA operon leader region

Contact Info

Product

Resources

About