Directed evolution of acyltransferases for the improvement of triglyceride production in Escherichia coli

Póster presentado al XXXVII Congreso de la Sociedad Española de Bioquímica y Biología Molecular, celebrado en Granada del 9 al 12 de septiembre de 2014.Wax ester synthase/diacylglicerol acyltransferase (WS/DGAT) is a family of enzymes able to perform the esterifi cation of diacylglycerol or fatty alcohols and acyl-CoA to produce triglycerides (TAGs) or wax esters, respectively. Both products can be easily transformed onto biodiesel. Although the specifi city determinants of substrate recognition are still unknown and there is no crystal structure solved from any bacterial WS/DGATs, we recently published a study where we used limited proteolysis and directed mutagenesis approaches to identify key folding domains and motifs critical for the catalysis. We have also recently patented a diacylglycerol acyltransferase (tDGAT) (ES201200967) from the thermophilic organism Thermomonospora curvata that is able to produce TAGs and waxes in E. coli. We have used this system for TAG production in E.coli, but we believe it can be signifi cantly improved through directed evolution of tDGAT. Thus, the main goal of our work is to enhance TAG production in E. coli by directed evolution. Moreover, this work will provide us some information about the amino acids residues involved in substrate recognition. For this purpose we have developed a direct evolution protocol where we constructed mutant libraries by mutagenic PCR in order to obtain variants of the protein. Using Nile Red, a fluorescent dye that binds to neutral lipids we can select different variants of tDGAT through a high throughput selection system based on fluorimetry and flow cytometry. Mutants carrying interesting phenotypes are further selected and sequenced. This way we were able to detect mutations that lead to a 2-fold increase in the TAG production.This work was supported by Ministerio de Ciencia e Innovación (BIO2010-240512).Peer Reviewe

Loading of malonyl-CoA Onto Tandem Acyl Carrier Protein Domains of Polyunsaturated Fatty Acid Synthases

Omega-3 polyunsaturated fatty acids (PUFA) are produced in some unicellular organisms, such as marine gammaproteobacteria, myxobacteria, and thraustochytrids, by large enzyme complexes called PUFA synthases. These enzymatic complexes resemble bacterial antibiotic-producing proteins known as polyketide synthases (PKS). One of the PUFA synthase subunits is a conserved large protein (PfaA in marine proteobacteria) that contains three to nine tandem acyl carrier protein (ACP) domains as well as condensation and modification domains. In this work, a study of the PfaA architecture and its ability to initiate the synthesis by selecting malonyl units has been carried out. As a result, we have observed a self-acylation ability in tandem ACPs whose biochemical mechanism differ from the previously described for type II PKS. The acyltransferase domain of PfaA showed a high selectivity for malonyl-CoA that efficiently loads onto the ACPs domains. These results, together with the structural organization predicted for PfaA, suggest that this protein plays a key role at early stages of the anaerobic pathway of PUFA synthesis

Alterations of OprD in carbapenem-intermediate and -susceptible strains of Pseudomonas aeruginosa isolated from patients with bacteremia in a Spanish multicenter study

Spanish Network for Research in Infectious Diseases (REIPI).-- et al.We investigated the presence of OprD mutations in 60 strains of metallo-ß-lactamase-negative Pseudomonas aeruginosa intermediately susceptible (IS [n = 12]; MIC = 8 μg/ml) or susceptible (S [n = 48]; MICs ≤ 1 to 4 μg/ml) to imipenem and/or meropenem that were isolated from patients with bacteremia in order to evaluate their impact on carbapenem susceptibility profiles. The presence of mutations in oprD was detected by sequencing analysis. OprD expression was assessed by both outer membrane protein (OMP) analysis and real-time PCR (RT-PCR). Fourteen (23%) isolates had an OprD identical to that of PAO1, and OprD modifications were detected in 46 isolates (77%). Isolates were classified as OprD “full-length types” (T1 [n = 40, including both wild-type OprD and variants showing several polymorphisms]) and OprD “deficient types” (T2 [n = 3 for OprD frameshift mutations] and T3 [n = 17 for premature stop codons in oprD]). RT-PCR showed that 5 OprD type T1 isolates presented reduced transcription of oprD (0.1- to 0.4-fold compared to PAO1), while oprD levels increased more than 2-fold over that seen with PAO1 in 4 OprD type T1 isolates. A total of 50% of the isolates belonging to OprD “deficient types” were susceptible to both carbapenems, and 40% were susceptible to meropenem and intermediately susceptible to imipenem. Only one isolate (5%) within this group was intermediately susceptible to both carbapenems, and one (5%) was susceptible to imipenem and intermediately susceptible to meropenem. We concluded that OprD inactivating mutations in clinical isolates of P. aeruginosa are not restricted only to carbapenem-resistant isolates but are also found in isolates with imipenem or meropenem MICs of only 0.06 to 4 μg/ml.This work was supported by the Ministerio de Ciencia e Innovación of Spain and Instituto de Salud Carlos III, through the Spanish Network for the Research in Infectious Diseases (REIPI C03/14 and RD06/0008), and grants PI08/0802, PS09/00033, and PI08/0276.Peer reviewe

Transcription factor-based biosensors enlightened by the analyte

Whole cell biosensors (WCBs) have multiple applications for environmental monitoring, detecting a wide range of pollutants. WCBs depend critically on the sensitivity and specificity of the transcription factor (TF) used to detect the analyte. We describe the mechanism of regulation and the structural and biochemical properties of TF families that are used, or could be used, for the development of environmental WCBs. Focusing on the chemical nature of the analyte, we review TFs that respond to aromatic compounds (XylS-AraC, XylR-NtrC, and LysR), metal ions (MerR, ArsR, DtxR, Fur, and NikR) or antibiotics (TetR and MarR). Analyzing the structural domains involved in DNA recognition, we highlight the similitudes in the DNA binding domains (DBDs) of these TF families. Opposite to DBDs, the wide range of analytes detected by TFs results in a diversity of structures at the effector binding domain. The modular architecture of TFs opens the possibility of engineering TFs with hybrid DNA and effector specificities. Yet, the lack of a crisp correlation between structural domains and specific functions makes this a challenging task.We are grateful to Spanish Ministry of Economy for Grant BIO2010-14809 to GM. Work in FdlC laboratory was financed by the Spanish Ministry of Economy and Competitivity (BFU2011-26608) and by the European Seventh Framework Program [projects 612146/FP7-ICT-2013-10 (PLASWIRES), 289326/KBBE-2011-5 (ST-FLOW) and 282004/FP7-HEALTH-2011-2.3.1-2 (EvoTAR)].USD 1,425 APC fee funded by the EC FP7 Post-Grant Open Access PilotPeer reviewe

A high security double lock and key mechanism in HUH relaxases controls oriT-processing for plasmid conjugation

This is an Open Access article distributed under the terms of the Creative Commons Attribution License.Relaxases act as DNA selection sieves in conjugative plasmid transfer. Most plasmid relaxases belong to the HUH endonuclease family. TrwC, the relaxase of plasmid R388, is the prototype of the HUH relaxase family, which also includes TraI of plasmid F. In this article we demonstrate that TrwC processes its target nic-site by means of a highly secure double lock and key mechanism. It is controlled both by TrwC-DNA intermolecular interactions and by intramolecular DNA interactions between several nic nucleotides. The sequence specificity map of the interaction between TrwC and DNA was determined by systematic mutagenesis using degenerate oligonucleotide libraries. The specificity map reveals the minimal nic sequence requirements for R388-based conjugation. Some nic-site sequence variants were still able to form the U-turn shape at the nic-site necessary for TrwC processing, as observed by X-ray crystallography. Moreover, purified TrwC relaxase effectively cleaved ssDNA as well as dsDNA substrates containing these mutant sequences. Since TrwC is able to catalyze DNA integration in anic-site-containing DNA molecule, characterization of nic-site functionally active sequence variants should improve the search quality of potential target sequences for relaxasemediated integration in any target genome.Spanish Ministry of Science and Innovation [BIO2010-14809 to G.M., BFU2011-26608 to F.C.]; European Union Seventh Framework Programme [612146/FP7-ICT-2013, 282004/FP7-HEALTH.2011.2.3.1-2 to F.C.]. Funding for open access charge: Spanish Ministry of Science and Innovation Grants [BIO2010-14809] and [BFU2011-26608].Peer Reviewe

A high security double lock and key mechanism in HUH relaxases controls oriT-processing for plasmid conjugation

Relaxases act as DNA selection sieves in conjugative plasmid transfer. Most plasmid relaxases belong to the HUH endonuclease family. TrwC, the relaxase of plasmid R388, is the prototype of the HUH relaxase family, which also includes TraI of plasmid F. In this article we demonstrate that TrwC processes its target nic-site by means of a highly secure double lock and key mechanism. It is controlled both by TrwC-DNA intermolecular interactions and by intramolecular DNA interactions between several nic nucleotides. The sequence specificity map of the interaction between TrwC and DNA was determined by systematic mutagenesis using degenerate oligonucleotide libraries. The specificity map reveals the minimal nic sequence requirements for R388-based conjugation. Some nic-site sequence variants were still able to form the U-turn shape at the nic-site necessary for TrwC processing, as observed by X-ray crystallography. Moreover, purified TrwC relaxase effectively cleaved ssDNA as well as dsDNA substrates containing these mutant sequences. Since TrwC is able to catalyze DNA integration in a nic-site-containing DNA molecule, characterization of nic-site functionally active sequence variants should improve the search quality of potential target sequences for relaxase-mediated integration in any target genome

Insights into the binding mode of lipid a to the anti-lipopolysaccharide factor ALFPm3 from penaeus monodon: an in silico study through MD simulations

The globally expanding threat of antibiotic resistance calls for the development of new strategies for abating Gram-negative bacterial infections. The use of extracorporeal blood cleansing devices with affinity sorbents to selectively capture bacterial lipopolysaccharide (LPS), which is the major constituent of Gram-negative bacterial outer membranes and the responsible agent for eliciting an exacerbated innate immune response in the host during infection, has received outstanding interest. For that purpose, molecules that bind tightly to LPS are required to functionalize the affinity sorbents. Particularly, anti-LPS factors (ALFs) are promising LPS-sequestrating molecules. Hence, in this work, molecular dynamics (MD) simulations are used to investigate the interaction mechanism and binding pose of the ALF isoform 3 from Penaeus monodon (ALFPm3), which is referred to as "AL3" for the sake of simplicity, and lipid A (LA, the component of LPS that represents its endotoxic principle). We concluded that hydrophobic interactions are responsible for AL3-LA binding and that LA binds to AL3 within the protein cavity, where it buries its aliphatic tails, whereas the negatively charged phosphate groups are exposed to the medium. AL3 residues that are key for its interaction with LA were identified, and their conservation in other ALFs (specifically Lys39 and Tyr49) was also analyzed. Additionally, based on the MD-derived results, we provide a picture of the possible AL3-LA interaction mechanism. Finally, an in vitro validation of the in silico predictions was performed. Overall, the insights gained from this work can guide the design of novel therapeutics for treating sepsis, since they may be significantly valuable for designing LPS-sequestrating molecules that could functionalize affinity sorbents to be used for extracorporeal blood detoxification.Financial support from the Spanish Ministry of Science, Innovation and Universities under the project RTI2018- 093310-B-I00 is gratefully acknowledged. C.G.F. also thanks the Spanish Ministry of Universities for the Margarita Salas postdoctoral fellowship (grants for the requalification of the Spanish university system for 2021−2023, University of Cantabria), funded by the European Union-NextGenerationEU

ArdC, a ssDNA-binding protein with a metalloprotease domain, overpasses the recipient hsdRMS restriction system broadening conjugation host range

Plasmids, when transferred by conjugation in natural environments, must overpass restriction-modification systems of the recipient cell. We demonstrate that protein ArdC, encoded by broad host range plasmid R388, was required for conjugation from Escherichia coli to Pseudomonas putida. Expression of ardC was required in the recipient cells, but not in the donor cells. Besides, ardC was not required for conjugation if the hsdRMS system was deleted in P. putida recipient cells. ardC was also required if the hsdRMS system was present in E. coli recipient cells. Thus, ArdC has antirestriction activity against the HsdRMS system and consequently broadens R388 plasmid host range. The crystal structure of ArdC was solved both in the absence and presence of Mn2+. ArdC is composed of a non-specific ssDNA binding N-terminal domain and a C-terminal metalloprotease domain, although the metalloprotease activity was not needed for the antirestriction function. We also observed by RNA-seq that ArdC-dependent conjugation triggered an SOS response in the P. putida recipient cells. Our findings give new insights, and open new questions, into the antirestriction strategies developed by plasmids to counteract bacterial restriction strategies and settle into new hosts.This work was supported by the Spanish Ministry of Economy, Industry and Competitiveness [BFU2014-55534-C2 to FdlC and GM] and by the Spanish Ministry of Education, Culture and Sports [FPU014/06013 to LG-M]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Structural basis of direct and inverted DNA sequence repeat recognition by helix-turn-helix transcription factors

Some transcription factors bind DNA motifs containing direct or inverted sequence repeats. Preference for each of these DNA topologies is dictated by structural constraints. Most prokaryotic regulators form symmetric oligomers, which require operators with a dyad structure. Binding to direct repeats requires breaking the internal symmetry, a property restricted to a few regulators, most of them from the AraC family. The KorA family of transcriptional repressors, involved in plasmid propagation and stability, includes members that form symmetric dimers and recognize inverted repeats. Our structural analyses show that ArdK, a member of this family, can form a symmetric dimer similar to that observed for KorA, yet it binds direct sequence repeats as a non-symmetric dimer. This is possible by the 180° rotation of one of the helix-turn-helix domains. We then probed and confirmed that ArdK shows affinity for an inverted repeat, which, surprisingly, is also recognized by a non-symmetrical dimer. Our results indicate that structural flexibility at different positions in the dimerization interface constrains transcription factors to bind DNA sequences with one of these two alternative DNA topologies.FUNDING This work was supported by the Spanish Ministry of Economy, Industry and Competitiveness [BIO2016-77883-C2-2- P and FIS2015-72574-EXP (AEI/FEDER, EU), to D.R.B., BFU2017-86378-P to F.dlC.] and by the Spanish Ministry of Science (MCI/AEI/FEDER,UE) [PGC2018-093885- BI00 and PID2021-122164NB-I00 to G.M., PID2020- 117028GB-I00 to D.R.B. and PID2019-110216GB-I00 to R. F-L.]. Conflict of interest statement. None declared. ACKNOWLEDGEMENTS Structural experiments were performed at the BL16 beamline at the ESRF European Synchrotron Radiation Facility (France) with the collaboration of EMBL staff, at the PROXIMA beamline at the SOLEIL Synchrotron (France) with the collaboration of SOLEIL staff, and at the XALOC beamline at the ALBA Synchrotron Radiation Facility (Spain) with the collaboration of ALBA staff. We are grateful to Carlos Revilla and Matilde Cabezas at the University of Cantabria for their technical assistance. Author contributions: R.F-L., F.dlC. and G.M. designed the research; L.G-M., R.R. and I.dC. performed the research; R.F-L., D.R.B., F.dlC and G.M analysed the data; and R.F.L., F.dlC. and G.M. wrote the manuscript. All authors reviewed the results and approved the final version of the manuscript

Design of Novel Relaxase Substrates Based on Rolling Circle Replicases for Bioconjugation to DNA Nanostructures

During bacterial conjugation and rolling circle replication, HUH endonucleases, respectively known as relaxases and replicases, form a covalent bond with ssDNA when they cleave their target sequence (nic site). Both protein families show structural similarity but limited amino acid identity. Moreover, the organization of the inverted repeat (IR) and the loop that shape the nic site differs in both proteins. Arguably, replicases cleave their target site more efficiently, while relaxases exert more biochemical control over the process. Here we show that engineering a relaxase target by mimicking the replicase target, results in enhanced formation of protein-DNA covalent complexes. Three widely different relaxases, which belong to MOBF, MOBQ and MOBP families, can properly cleave DNA sequences with permuted target sequences. Collaterally, the secondary structure that the permuted targets acquired within a supercoiled plasmid DNA resulted in poor conjugation frequencies underlying the importance of relaxase accessory proteins in conjugative DNA processing. Our results reveal that relaxase and replicase targets can be interchangeable in vitro. The new Rep substrates provide new bioconjugation tools for the design of sophisticated DNA-protein nanostructures.This work was financed by grants BFU2014-55534-C2-1-P from the Spanish Ministry of Economy and Competitiveness and 612146/FP7-ICT- 2013 and 282004/FP7-HEALTH.2011.2.3.1-2 from the European Union Seventh Framework Programme to FC and grant BFU2014-55534-C2-2-P from the Spanish Ministry of Economy and Competitiveness to GM. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript