Insights into the evolution of enzyme substrate promiscuity after the discovery of (βα)₈ isomerase evolutionary intermediates from a diverse metagenome.

Gabriela Montero-Moran
Gabriela Montero-Moran
The State University of New Jersey
United States
Dr. Mauricio Carrillo-Tripp, PhD
Dr. Mauricio Carrillo-Tripp, PhD
Biomolecular Diversity Laboratory, Cinvestav
Associate Profesor
Computational Biophysics
Irapuato, Guanajuato | México

BMC Evol Biol 2015 Jun 10;15:107. Epub 2015 Jun 10.

Evolution of Metabolic Diversity, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Km 9.6 Libramiento Norte, Carretera Irapuato - León, CP 36821, Irapuato, México.

Background: Current sequence-based approaches to identify enzyme functional shifts, such as enzyme promiscuity, have proven to be highly dependent on a priori functional knowledge, hampering our ability to reconstruct evolutionary history behind these mechanisms. Hidden Markov Model (HMM) profiles, broadly used to classify enzyme families, can be useful to distinguish between closely related enzyme families with different specificities. The (βα)8-isomerase HisA/PriA enzyme family, involved in L-histidine (HisA, mono-substrate) biosynthesis in most bacteria and plants, but also in L-tryptophan (HisA/TrpF or PriA, dual-substrate) biosynthesis in most Actinobacteria, has been used as model system to explore evolutionary hypotheses and therefore has a considerable amount of evolutionary, functional and structural knowledge available. We searched for functional evolutionary intermediates between the HisA and PriA enzyme families in order to understand the functional divergence between these families.

Results: We constructed a HMM profile that correctly classifies sequences of unknown function into the HisA and PriA enzyme sub-families. Using this HMM profile, we mined a large metagenome to identify plausible evolutionary intermediate sequences between HisA and PriA. These sequences were used to perform phylogenetic reconstructions and to identify functionally conserved amino acids. Biochemical characterization of one selected enzyme (CAM1) with a mutation within the functionally essential N-terminus phosphate-binding site, namely, an alanine instead of a glycine in HisA or a serine in PriA, showed that this evolutionary intermediate has dual-substrate specificity. Moreover, site-directed mutagenesis of this alanine residue, either backwards into a glycine or forward into a serine, revealed the robustness of this enzyme. None of these mutations, presumably upon functionally essential amino acids, significantly abolished its enzyme activities. A truncated version of this enzyme (CAM2) predicted to adopt a (βα)6-fold, and thus entirely lacking a C-terminus phosphate-binding site, was identified and shown to have HisA activity.

Conclusion: As expected, reconstruction of the evolution of PriA from HisA with HMM profiles suggest that functional shifts involve mutations in evolutionarily intermediate enzymes of otherwise functionally essential residues or motifs. These results are in agreement with a link between promiscuous enzymes and intragenic epistasis. HMM provides a convenient approach for gaining insights into these evolutionary processes.

Download full-text PDF

Source Listing

Still can't find the full text of the article?

Sign up to send a request to the authors directly.
June 2015
55 Reads
5 PubMed Central Citations(source)
3.37 Impact Factor

Publication Analysis

Top Keywords

functionally essential
enzyme families
hisa pria
evolutionary intermediate
hmm profile
functional shifts
pria enzyme
hmm profiles
amino acids
evolutionary intermediates
phosphate-binding site
biochemical characterization
acids biochemical
characterization selected


(Supplied by CrossRef)
Article in Curr Opin Chem Biol
O Khersonsky et al.
Curr Opin Chem Biol 2006
Article in Annu Rev Biochem
O Khersonsky et al.
Annu Rev Biochem 2010
Article in Proc Natl Acad Sci U S A
RA Notebaart et al.
Proc Natl Acad Sci U S A 2014
Article in Annu Rev Microbiol
RA Jensen et al.
Annu Rev Microbiol 1976
Article in Nat Rev Genet
M Soskine et al.
Nat Rev Genet 2010
Article in Proc Natl Acad Sci U S A
RQ Huang et al.
Proc Natl Acad Sci U S A 2012
Article in Biochem J
JM Sanchez-Ruiz et al.
Biochem J 2012
Article in Mol Biol Evol
M Parera et al.
Mol Biol Evol 2014
Article in Biochem J
W Zhang et al.
Biochem J 2012

Similar Publications

A Novel Electroactive Agarose-Aniline Pentamer Platform as a Potential Candidate for Neural Tissue Engineering.

Sci Rep 2017 Dec 7;7(1):17187. Epub 2017 Dec 7.

Center of Excellence in Electrochemistry, School of Chemistry, College of Science, University of Tehran, Tehran, Iran.

Neuronal disorder is an important health challenge due to inadequate natural regeneration, which has been responded by tissue engineering, particularly with conductive materials. A bifunctional electroactive scaffold having agarose biodegradable and aniline pentamer (AP) conductive parts was designed that exhibits appropriate cell attachment/compatibility, as detected by PC12 cell seeding. The developed carboxyl-capped aniline-pentamer improved agarose cell adhesion potential, also the conductivity of scaffold was in the order 10 S/cm reported for cell membrane. Read More

View Article
December 2017
7 Reads
5.08 Impact Factor

CRISPR-based strategies for studying regulatory elements and chromatin structure in mammalian gene control.

Mamm Genome 2018 04 1;29(3-4):205-228. Epub 2017 Dec 1.

Department of Genetics, Albert Einstein College of Medicine, Michael F. Price Center, 1301 Morris Park Avenue, Room 475, Bronx, NY, 10461, USA.

The development of high-throughput methods has enabled the genome-wide identification of putative regulatory elements in a wide variety of mammalian cells at an unprecedented resolution. Extensive genomic studies have revealed the important role of regulatory elements and genetic variation therein in disease formation and risk. In most cases, there is only correlative evidence for the roles of these elements and non-coding changes within these elements in pathogenesis. Read More

View Article
April 2018
52 Reads
3.07 Impact Factor

Characteristics of fatal and hospital admissions for burns in Fiji: a population-based study (TRIP Project-2).

Burns 2012 Aug 17;38(5):758-62. Epub 2012 Feb 17.

Research Unit, College of Medicine, Nursing and Health Science, Fiji National University, Suva, Fiji.

Background: Over 95% of burn deaths are estimated to occur in low-and-middle-income countries. However, the epidemiology of burn-related injuries in Pacific Island Countries is unclear. This study investigated the incidence and demographic characteristics associated with fatal and hospitalised burns in Fiji. Read More

View Article
August 2012
6 Reads
1 PubMed Central Citation(source)
1.84 Impact Factor

Advanced techniques for penetration enhancement in transdermal drug delivery system.

Curr Drug Deliv 2011 Jul;8(4):456-73

Department of Pharmaceutics, Roland Institute of Pharmaceutical Sciences, Khodasingi, Berhampur-760010 (Gm), Orissa, India.

Transdermal route has been recognized as a promising drug delivery system for systemic delivery of drugs and provides the advantage of avoidance of first-pass effect, ease of use, better patient compliance, maintaining constant blood level for longer period of time and decrease side effects. The major pitfalls of this route lie with difficulty in permeation of drugs through the skin. Several literatures have been published for enhancing the permeation of drugs by chemical approaches. Read More

View Article
July 2011
9 Reads
2 PubMed Central Citations(source)
2.25 Impact Factor

Association of temporal trends in risk factors and treatment uptake with coronary heart disease mortality, 1994-2005.

JAMA 2010 May;303(18):1841-7

Division of Cardiology, Schulich Heart Centre, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada.

Context: Coronary heart disease (CHD) mortality has declined substantially in Canada since 1994.

Objective: To determine what proportion of this decline was associated with temporal trends in CHD risk factors and advancements in medical treatments.

Design, Setting, And Patients: Prospective analytic study of the Ontario, Canada, population aged 25 to 84 years between 1994 and 2005, using an updated version of the validated IMPACT model, which integrates data on population size, CHD mortality, risk factors, and treatment uptake changes. Read More

View Article
May 2010
12 Reads
76 PubMed Central Citations(source)
35.29 Impact Factor