Structural and Biochemical Characterization of AaL, a Quorum Quenching Lactonase with Unusual Kinetic Properties
Authors: Tanushree Naik
David Daudé
Mikael Elias
Eric Chabrière
Celine Bergonzi
Michael Schwab
Journal: Scientific Reports (2018)
Discipline: Multidisciplinary
Keywords: Quorum quenching lactonases; bacterial signaling; acyl homoserine lactones (AHL); biofilms; virulence factors
Affiliations: Biochemistry, Molecular Biology & Biophysics Dpt and BioTechnology Institute, University of Minnesota, Saint Paul, Minnesota, 55108, USA., Gene&GreenTK, 19-21 Boulevard Jean Moulin, 13005, Marseille, France., Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France., Biochemistry, Molecular Biology & Biophysics Dpt and BioTechnology Institute, University of Minnesota, Saint Paul, Minnesota, 55108, USA. .

Abstract:  Quorum quenching lactonases are enzymes that are capable of disrupting bacterial signaling based on acyl homoserine lactones (AHL) via their enzymatic degradation. In particular, lactonases have therefore been demonstrated to inhibit bacterial behaviors that depend on these chemicals, such as the formation of biofilms or the expression of virulence factors. Here we characterized biochemically and structurally a novel representative from the metallo-β-lactamase superfamily, named AaL that was isolated from the thermoacidophilic bacterium Alicyclobacillus acidoterrestris. AaL is a potent quorum quenching enzyme as demonstrated by its ability to inhibit the biofilm formation of Acinetobacter baumannii. Kinetic studies demonstrate that AaL is both a proficient and a broad spectrum enzyme, being capable of hydrolyzing a wide range of lactones with high rates (kcat/KM &gt; 105 M-1.s-1). Additionally, AaL exhibits unusually low KM values, ranging from 10 to 80 µM. Analysis of AaL structures bound to phosphate, glycerol, and C6-AHL reveals a unique hydrophobic patch (W26, F87 and I237), involved in substrate binding, possibly accounting for the enzyme's high specificity. Identifying the specificity determinants will aid the development of highly specific quorum quenching enzymes as potential therapeutics. 

Retracted: No

PubPeer comments:
 Dear Dr. Bik, Your harassment on pubpeer on our research articles, as evidenced by your last statement u201cBased on recent social media activities, author EC appears to be very interested in pointing out other authors conflict of interest. Could he or other authors please comment on this perceived conflict?u201d does not honor you. 1.tThis startup company that I co-founded owns IP for mutants on the SsoPox enzyme (WO2014167140A1), not AaL enzyme. 2.tThe two enzymes (AaL and SsoPox) are unrelated, and do not even align in sequence. 3.tThe enzyme discussed in the paper is a wild-type protein, on which no financial interest exists. , 
 From the Abstract:  Here we characterized biochemically and structurally a novel representative from the metallo-u03b2-lactamase superfamily, named AaL that was isolated from the thermoacidophilic bacterium Alicyclobacillus acidoterrestris. AaL is a potent quorum quenching enzyme as demonstrated by its ability to inhibit the biofilm formation of Acinetobacter baumannii (...) Identifying the specificity determinants will aid the development of highly specific quorum quenching enzymes as potential therapeutics. From the Additional Information:  Competing Interests: The authors declare no competing interests. However, the two last authors did not disclose that they are founders of a biotech company called  Gene GreenTK , which was founded in 2013, thus pre-dating the submission of this paper. The company s expertise appears very relevant to the enzyme described in the paper. Some quotes from their website https: www.gene-greentk.com (archived: https: archive.is 6Gr1R) : *  The work of G G is dedicated to the development and engineering of enzymes isolated from microorganisms living in extreme environments. *  We develop enzymes that ally both perfomance [sic] and stability. Coming straight from extreme environments and produced by hyperthermophilic microorganisms. *  Bacteria use chemical signals to communicate and coordinate behaviors including virulence and biofilm formation. Our technology interrupts bacterial communication by degrading signal molecules thereby preventing bacteria from forming biofilms and to start a virulence program. *  Anti-virulence and anti-biofilm for the development of novel medical devices, anti-fouling paintings or coatings and biobased materials ![file] Based on recent social media activities (e.g. https: archive.is FI9sH - https: archive.is RWmwF - https: archive.is 0hECd), one of the authors appears to be very interested in pointing out other authors conflicts of interest. Could he or other authors please comment on this perceived conflict? , 
 #2 In another [2018 paper](10.1038 s41598-018-28988-5) the conflict of interest disclosure reads: ![file] The current journal policies regarding conflicts of interest are below: **Competing interests** Competing interests policy In the interests of transparency and to help readers to form their own judgements of potential bias, authors must declare any competing financial and or non-financial interests in relation to the work described. Definition of a competing interest For the purposes of this policy, competing interests are defined as financial and non-financial interests that could directly undermine, or be perceived to undermine, the objectivity, integrity and value of a publication, through a potential influence on the judgements and actions of authors with regard to objective data presentation, analysis and interpretation. Financial competing interests include any of the following: Funding: Research support (including salaries, equipment, supplies, and other expenses) by organizations that may gain or lose financially through this publication. A specific role for the funder in the conceptualization, design, data collection, analysis, decision to publish, or preparation of the manuscript, should be disclosed. Employment: Recent (while engaged in the research project), present or anticipated employment by any organization that may gain or lose financially through this publication. Personal financial interests: Stocks or shares in companies that may gain or lose financially through publication; consultation fees or other forms of remuneration (including reimbursements for attending symposia) from organizations that may gain or lose financially; patents or patent applications (awarded or pending) filed by the authors or their institutions whose value may be affected by publication. For patents and patent applications, disclosure of the following information is requested: patent applicant (whether author or institution), name of inventor(s), application number, status of application, specific aspect of manuscript covered in patent application. It is difficult to specify a threshold at which a financial interest becomes significant, but note that many US universities require faculty members to disclose interests exceeding $10,000 or 5% equity in a company (see, for example, B. Lo et al. New Engl. J. Med. 343, 1616-1620; 2000). Any such figure is necessarily arbitrary, so we offer as one possible practical alternative guideline:  Any undeclared competing financial interests that could embarrass you were they to become publicly known after your work was published. We do not consider diversified mutual funds or investment trusts to constitute a competing financial interest. Non-financial competing interests: Non-financial competing interests can take different forms, including personal or professional relations with organizations and individuals. We would encourage authors and referees to declare any unpaid roles or relationships that might have a bearing on the publication process. Examples of non-financial competing interests include (but are not limited to): - Unpaid membership in a government or non-governmental organization - Unpaid membership in an advocacy or lobbying organization - Unpaid advisory position in a commercial organization - Writing or consulting for an educational company - Acting as an expert witness ,