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Thursday 19 December 2013

Degradation of nitrile-containing ionic liquids but how?


It is well known that soil bacteria and fungi bioremediate nitrile containing compounds to get at their nitrogen, and that nitrilase/nitrile hydratase pathway enzymes in a range of bacteria/fungi are amenable to such a transformation. A colleague of mine, Steve Cummings, reviewed this area a few years back in a paper entitled "The current and future applications of microorganisms in the bioremediation of cyanide contamination". One possible source of environmental cyanide contamination that Steve didn’t foresee was that from ionic liquids. These have been the subject of a lot of enthusiasm in green chemistry circles as they offer immensely useful solvation properties with no appreciable vapour pressure. Their use on anything other than a laboratory bench scale has met some resistance because of concerns about their environmental toxity. A recent paper entitled “Biodegradation potential of cyano-based ionic liquid anions in a culture of Cupriavidus spp. and their in vitro enzymatic hydrolysisby nitrile hydratase” by Stefan Stolte and co-workers in Environmental Science and Pollution Research has looked at biological hydration/hydrolysis of ionic liquids containing cyano groups.


After trying an organism, they have used a couple of Sigma enzymes to see if these will process their choice of ILs. They discover that the Sigma nitrilase isn’t interested but the Sigma NHase is quite happy to turnover. But I do wish that this information went further. Sigma does not tell you what the source organism(s) for their Nase and NHase enzymes is/are, merely that they are recombinant from E. coli. There is so much variation in substrate selectivity for both classes (for instance, glance at the slice of Steve’s Table 1 below) that getting a positive or a negative hit from a single example of unknown origin tells you not much at all in general.

Tuesday 10 December 2013

Sol-gel encapsulation of Cobalt centred nitrile hydratase

The nitrile hydratase from Pseudonocardia thermophila is one of the most stable NHases currently described. It is cobalt centred, and one strain of it has an entry in the PDB. Holz and co-workers have just published a paper entitled "Acrylamide Production using Encapsulated Nitrile Hydratase from Pseudonocardia thermophila in a Sol-gel matrix" in the Journal of Molecular Catalysis A. They show that their system is able to convert acrylonitrile to acrylamide neatly, demonstrating the advantages of their enzyme support system in terms of increasing the robustness of these still rather sensitive enzymes. Interesting to me is that their orthosilicate sol-gels boost this enzyme's stability in methanol to take as much as a70% v/v mix happily.


Nitrile hydratase in March's Advanced Organic Chemistry

As a graduate student, March's Advanced Organic Chemistry was my "go-to" text for leading references for synthetic chemistry questions. It was an incredibly thick book with an extraordinary number of references, and it has only increased in size since my days in TCD, and it is now in its seventh edition.
As my indexing system these days needs more key strokes to navigate than is needed to find things on the Web using Google, I decided to find my first paper on nitrile hydratase online to see which substrates I should have in my "interesting nitriles" cupboard which were ortho-substituted. Sure enough the paper was there but so also was a link to that paper as a reference in March. Yes, it's reference 103 on page 1080 of the seventh edition, as a reference to consult about amide formation though the reason for its inclusion is a bit weird. Anyway, I am very pleased!

Thursday 5 December 2013

Making an approximate 3D model of an enzyme

Sometimes we want to check out how an amino acid sequence from a database might translate into a 3D dimensional structure. This is straightforward enough if there exists an x-ray crystal structure for that exact enzyme in the Protein Data Bank or, like often happens in the nitrile hydratase class, there is very limited variation within sequences so overlaying a short portion of the sequence "by eye" on an existing enzyme is possible.
We are currently working on nitrilases, and despite increasing interest in their use as biocatalysts, the number of nitrilases (i.e. enzymes that convert nitriles to carboxylic acids not the other looser biochemical definition) which exist as structures in the PDB s precisely one. It is from Pyrococcus abyssi and is pretty much restricted in substrate tolerance to small aliphatic nitriles like fumaronitrile. It should not be a surprise that it isnt a great model for many other nitrilases.
If the PDB has come up short we tend to use a link out of the Uniprot database to give a prediction of 3D structure. So if you want to see an estimate of what the nitrilase from Aurantimonas manganoxydans looks like, than the link labelled "ModBase" under the subtitle "3D structure databases" leads you to a page of predictions and further tools. For this specific enzyme it is suggested that a mouse nitrilase superfamily structure contains the best 3D match.

Thursday 28 November 2013

A nitrile hydratase for cyanopyridines... and it's a bit more stable than usual.


There is a paper in Process Biochemistry which describes a new NHase from Aurantimonas manganoxydans which shows improved stability than you can normally expect from a NHase. It is entitled “Efficient cloning and expression of a thermostable nitrile hydratase in Escherichia coli using an auto-induction fed-batch strategy”, and it is by Xiaolin Peia, Hongyu Zhang, Lijun Meng, Gang Xu, Lirong Yang and Jianping Wu. This NHase is four times more rapid at converting 3-cyanopyridine to its corresponding amide as valeronitrile, and the authors emphasize their enzyme's stability though in the world of NHases where nothing is what you might describe as thermophilic, please don't get too expectant! They have a great table of NHase thermostability which I reproduce with their enzyme's data inserted.
 

A nitrile hydratase for cyanopyridines... (but it prefers aliphatic nitriles)


There has been a recent paper in Journal of Molecular Catalysis B on a nitrilase that converted cyanopyridines. This enzyme came from a strain of Pseudomonas putida. There is also a recent paper in the same journal entitled “Discovery of a new Fe-type nitrile hydratase efficiently hydrating aliphatic and aromatic nitriles by genome mining” by Xiaolin Peia, Lirong Yang, Gang Xu, Qiuyan Wang and Jianping Wu.which describes a nitrile hydratase, this time, from a Pseudomonas putida strain (F1) which they have shown to be able to turn over 3-cyanopyridine in a 1L fed batch reactor. Their activity data suggests it actually prefers aliphatic nitriles: acrylonitrile rates as 941 U/mg and valeronitrile as 535 U/mg as compared to 3-cyanopyridine at 26 U/mg. They describe how it was cloned into E. coli, needing the inclusion of an activator protein to get activity. They also include a nice phylogenetic tree showing the spread of known iron type NHases... plenty of examples in the Rhodococcus but spreading outwards into Pseudomonas.

Tuesday 12 November 2013

Scaling up a nitrilase based hydrolysis


Efficient Production of (R)-o-Chloromandelic Acid by Recombinant Escherichia coli Cells Harboring Nitrilase from Burkholderia cenocepacia J2315 by Dongzhi Wei and co-workers is published in Organic Process Research and Development at  DOI:10.1021/op400174a.  It being OPRD and from a group working in a Laboratory of Bioreactor Engineering, it’s going to be an interesting read on doing a nitrilase reaction on the larger scale.  We are currently working on scaling up a different nitrilase-based reaction currently from bench scale to the “too heavy to use normal glassware” scale so it’s good to see how others do it.
 

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A nitrilase for cyanopyridines...


Characterization and functional cloning of an aromatic nitrilase from Pseudomonas putida CGMCC3830 with high conversion efficiency toward cyanopyridine by Hong Xu and co-workers in Journal of Molecular Catalysis B: Enzymatic is the first report of cloning of an aromatic nitrilase from Pseudomonas genus. It has a particular penchant for 3-cyanopyridine.

Friday 30 August 2013

Zaparucha nitrilase activities

One of the joys of the Zaparucha nitrilase paper recently published in Advanced Synthesis and Catalysis is that their search for nitrilase activity is not confined to those enzymes which have already been automated annotated as "nitrilase". Within their enzyme set are proteins annotated as amidases, cyanide hydrolases, ureidopropionases, hydrolases (nice and broad that!) and even glycosyl. Here is my analysis of their protein types done by text searching their supplementary materials.




Text search strings are across the top and obviously "nitrilase" will also find those in "nitrilase/cyanide", and "hydrolase" occurs all over the shop. The second line indicates the totals after my removal of those proteins which didnt show any nitrilase activity for them. (You can take the chemist stance "something wrong with the protein" or the molecular biologists stance "you havent found the right substrate yet" at your own whim!). A very interesting set of annotations!

 

Selectivity in nitrilases

One of the things we are interested in looking at with our increasingly wide panel of nitrilases is how substrate selectivity works with classic Group 1 nitrilases.
 Our standard panel of substrates we are assaying our nitrilases against has fifty substrates so we span quite a range of different structural types and traits. Here is an excerpt from our posters' table of data.


Colour coding mirrors the response that we see with our assay and carries handy semi-quantitative values as well which we get from UV/vis spectroscopy. What we have here is a table with different substrates along the top and different nitrilases down the side.
The top row here shows a nitrilase which hydrolyzes arylaliphatic substrates with great gusto (showing a 10 against 2-phenylacetonitrile) but has not a lot of interest in alkyl or aryl nitriles generally. The fifth row shows a nitrilase which is an enthusiast for aromatic nitriles peaking at para-substituted aromatics but with some interest in almost everything else!
To some extent the other patterns of activties are also interesting... we see some nitrilases which show activities which are active against only a few compounds which are quite structurally diverse. This may be a low expression level only letting us see the most active members of wider groupings (because this data table comes out of a screening programme of cell-free extracts), and this is something we will be investigating. It would be nice to hope that there was something a bit deeper going on though.
Finally we have some enzymes like one in the fourth line here which appear to be oblivious to everything. These show up a difference of response within our team. I, as the chemist, say "perhaps it just isn't active at all"; our molecular biologists say "nonsense- with that sequence it's just got to be a nitrilase, you haven't found the right substrate yet"!
We'll keep looking... for new nitrilases and new substrates.

Tuesday 23 July 2013

Nitrile active enzyme posters

We are at Biotrans 2013 in Manchester this week. Whilst it has to be said that transaminases is the most frequently described enzyme type described here, there are a few posters describing nitrile active enzymes.
Nicola D'Antona has a poster entitled "Biotransformations of nitrile ferrocenes catalyzed by the bienzymatic system of nitrile hydratase/amidase: first examples of molecular recognition and enantioselectivity of chiral planar substrates". This poster describes the use of a couple of Rhodococcus species to hydrate and hydrolyze either one or two cyano groups appended to the double decker ferrocene sandwich. Considering NHases' dislike of bulky substrates that is a neat discovery. They even get some enantioselectivity especially in the acids where the amidase in the whole cell is strongly selective in determining the sterics of the outcome.
Birgit Wilding has a poster entitled "Enantioselective synthesis of a taxol side chain precursor with bacterial and fungal nitrilases". Obviously finding a biocatalytic way to build even a portion of a pharmaceutical is a great demonstration of using this technology to provide a green and inherently stereoselective route for the commercial arena. An interesting finding reported on this poster is the tendency of the bacterial nitrilases (two of which came from our Nzomics panel) in her panel to serve up not just the acid but the primary amide of her side chain precursors too. The ratio of amide to acid is sensitive to substrate concentration... Intriguing- I had one person previously complain about getting amide when they wanted acid with one of these enzymes but I don't know what their substrate was!
Cintia Milagre is displaying a poster called "Synthesis of alkyl and aryl substituted amides by nitrile hydratases" summarizing work on nitrile hydratase discovery from Brazilian soil samples and their utility at hydrating alpha substituted nitriles.
Carine Vergne-Vaxelaire is displaying a poster entitled "Biocatalytic tools for organic chemists: new nitrilases for synthesis of building blocks" which outlines the high throughput screening of 125 nitrilases against 25 structurally diverse nitriles, and is linked to a lecture being given later in the week by Anne Zaparucha.
Sander van Pelt has a poster called "Nitrile Hydratases: from genes to immobilized biocatalyst" highlighting the extra utility that a covalently linked enzyme aggregate preparation from CLEA Technologies has in terms of stability. It is nice to see that the NHases from AJ270 and CGA009 that we have worked on together are still useful examples in this field.
Finally hiding undercover at P387 is our poster on nitrilases. Graeme Turnbull has written up his semi-quantitative colorimetric methodology for assaying the activity of nitrilases as cell-free extracts (which screw up a pH driven colorimetric method) and then showing how he has applied it to a panel of 14 enzymes and 40 diverse substrates.

Friday 19 July 2013

Poster at Biotrans2013

We'll be at Biotrans 2013 in Manchester next week showing a poster entitled "A novel, high-throughput screening method for group 1 nitrilase activity" which gives an outline of how we screen our nitrilases (as cell free extracts) colorimetrically against substrates on 96 well plates.

 

New mini-review on genome mining for nitrilases

In Applied Microbiology and Biotechnology's August 2013 issue, there is a mini review entitled "Metagenomic technology and genome mining: emerging areas for exploring novel nitrilases" from G-S Gong et al which will be relevant for nitrilase fanatics (DOI 10.1007/s00253-013-4932-8).

Thursday 11 July 2013

Animated GIF of 3IVZ

Using the useful PDB2MultiGIF page, this is a rotating image of the Pyroccocus abyssi GE5 PDB file 3IVZ.


What's in a name?

Despite the fact that the term "nitrilase" seems to have quite an obvious origin using the obvious enzyme naming template that a chemist might use (nitrilase = nitrile + ase... so must be something that acts on nitriles), there is a flaw in this. "Nitrilase" has actually been taken by biologists to mean a class of similar enzymes that attack molecules with C-N bonds. In fact, it is only Group 1 nitrilases actually do the "nitrile to carboxylic acid" conversion which we are currently working on, and the other groups which do other types of C-N bond breaking reactions. Table 1 in Charles Brenner's 2002 "Catalysis in the Nitrilase Superfamily" review in Current Opinions in Structural Opinions shows the breadth of other chemistries that appear in the nitrilase superfamily.This broad use of a name explains why there are so many PDB files listed for a search for "nitrilase" which do not actually do the nitrile-acid conversion as well as why there is great confusion between nitrile hydratase and nitrilase activities in many databases.

If you look through the 29 PDB files which are labelled as nitrilase, there is in fact only one enzyme which is a Group 1 nitrilase- and that is the nitrilase from the hyperthermophile Pyrococcus abyssi GE5 (this is an example of a PDB of this enzyme) which was described in a 2011 Journal of Structural Biology paper (doi: 10.1016/j.jsb.2010.11.017) by Rypniewski. As Martinkova has commented in her 2010 Current Opinions in Chemical Biology review (doi: 10.1016/j.cbpa.2009.11.018), this lack of crystal structures made structure–function relationship studies for nitrilases difficult.

Tuesday 2 July 2013

How specific are nitrilases for their substrates?

As part of our ongoing nitrilase discovery project, we are trying a panel of about 50 substrates of various types against an ever-growing panel of nitrilases. The first round panel has 20 enzymes, and using a chromogenic assay we are seeing the rather nice selectivity that the literature indicates these enzymes show. Below, an example of two nitrilases (with each repeated) and their response to 4 simple nitriles- the depth of colour scales nicely with the amount of ammonia released by the nitrile hydrolysis.



There are similar levels of diversity of response for aryl over alkyl nitriles, and short chain over long chain nitriles. After the colour screening we are moving onto GCMS for confirmatory results, as well as doing a bit of NMR for that final structural evidence.

Tuesday 18 June 2013

125 Nitrilase activities all in the one place.

Imagine you are working on a panel of enzymes and their activities against a library of substrates looking to try to link substrate specificity to microbial origin, and then someone comes along and publishes a very similar thing…. Argh! Let me recommend to you Nitrilase Activity Screening on Structurally Diverse Substrates Providing Biocatalytic Tools for Organic Synthesis by fourteen authors  with corresponding author Anne Zaparucha, which is in Advanced Synthesis and Catalysis at DOI:10.1002/adsc.201201098.
It is good to see that full information is given on the nature of the nitrilases (Uniprot codes are given for each NIT reference) and they have a neat assay for nitrilase activity. Obviously a working nitrilase kicks out ammonia stoichiometrically so that's the best thing to be looking for in an activity assay. There are several ways to do this (for example pH change has been advocated e.g. Banerjee's bromothymol blue screen in J Biomol Screen at DOI: 10.1177/1087057103256910 but we have found it not to work for cell free extract based enzymes- too many other endogenous sources of pH change I'd guess) but this paper describes a nice coupled assay which uses the evolved ammonia as a substrate for a glutamate dehydrogenase with readout through the level of NADH/NAD+.


We are currently assaying nitrilase sequence space (as the jargon that got us the grant says!) as well. Our first round involves twenty enzymes and fifty substrates... we will be adding to the number of enzymes but we think 50 substrates sounds about right to assess selectivity. We have our own assay methodology which seems to give about the level of activity readout we want for a semiquantitative read on a plate reader... here's an example- top row shows a colour chart of increasing activity, the rest of the wells are substrates with a single enzyme.

 

Can genes be patented?

This article reports on the American Supreme Court ruling about the ability to patent DNA sequences from a genome. It can't be done now. That is sensible. Being able to patent genes on discovery can only stiffle innovation and fund legal process not research.

New nitrile hydratase papers


Enzyme–Substrate Binding Landscapes in the Process of Nitrile Biodegradation Mediated by Nitrile Hydratase and Amidase from Yu Zhang, Zhuotong Zeng, Guangming Zeng, Xuanming Liu, Ming Chen, Lifeng Liu, Zhifeng Liu & Gengxin Xie in Applied Biochemistry and Biotechnology describes molecular modelling experiments using the crystal structures 2QDY (AJ270 Fe based NHase) and 1IRE (Pseudonocardia thermophila Co based NHase).This is a docking study for these two enzymes and a downstream amidase. Available at DOI 10.1007/s12010-013-0276-1. Shown below is Fig1b which illustrates a binding mode between the P. thermophila Co based NHase and 3-cyanopyridine.



Strategy for successful expression of the Pseudomonas putida nitrile hydratase activator P14K in Escherichia coli by Yi Liu, Wenjing Cui , Yueqin Fang, Yuechun Yu, Youtian Cui, Yuanyuan Xia, Michihiko Kobayashi and Zhemin Zhou adds to debate around the activator which is used for the maturation of the NHase with inclusion of the metal centre  (they say an activator is always needed, but is that true?). This paper is found in BMC Biotechnology at DOI:10.1186/1472-6750-13-48 and describes a methodology to ensure that the P14K activator is expressed successfully and in a more stable form.

Friday 31 May 2013

NHase numbers to May 2013, and now nitrilase numbers too

Looking at the bare search term "nitrile hydratase" amongst protein sequences (and remember, most aren’t but it’s a rough measure), today gives me 4782 hits (+ 14% since last November), of which 2440 (+ 50% since August) were RefSeq data. It appears that there has been a lot of RefSeq going on with this enzyme class.
There are 24848 sequences labelled as "nitrilase" (not sure how robust that is currently), of which 12037 are pegged as RefSeq data.

Tuesday 21 May 2013

An example of gentle hydration using a nitrile hydratase

Using an extreme of pH to carve up a nitrile bond is going to be problematic when there are other, sensitive parts to a molecule. An example would be a nitrile appended to a ferrocene. D'Antona and coworkers are reporting the use of the nitrile hydratase from two Rhodococcus erythropolis strains in whole cell mode to convert nitrile to amide. [DOI:10.1039/C3RA22737E]. The presence of an amidase in the whole cell then coverts a minority through to the related carboxylic acid.

Wednesday 15 May 2013

Slight pivot

I have been doing this blog for 2 years and just over 100 posts, and over that time I have focussed very narrowly on nitrile hydratases. Whilst they are lovely enzymes and I will continue to work on/with them, a growing interest of mine has become their cousins, the nitrilases. I now have more research effort going into nitrilases than nitrile hydratases, so from henceforth I intend to write about NHases and nitrilases. I don't think I am going to stretch to amidases, even if they are on the same operon (or whatever molecular biologists call it!). Just to add a bit of contemporary experimental data to the usual reports, I intend to report some interesting and as yet unreported results here (obviously without compromising my ability to publish them eventually) on an ongoing nitrilase discovery project as they happen.

What might happen after the nitrile hydratase has done its job in a whole cell system?

...You've got to work with the amidase which converts the amide to the corresponding carboxylic acid.
Laura Cantarella, Alberto Gallifuoco, Agata Spera and Maria Cantarella look at the amidase in the NHase/amidase system of Microbacterium imperiale CBS 498-74 in the paper entitled "Nitrile, amide and temperature effects on amidase-kinetics during acrylonitrile bioconversion by nitrile-hydratase/amidase in-situ cascade system" in the journal Bioresource Technology with DOI:10.1016/j.biortech.2013.04.126.

E. coli expression of active nitrile hydratase from Aurantimonas manganoxydans needs cobalt ions

This paper in Biotechnology Letters from Pei and co-workers gives details of a cobalt centred nitrile hydratase from Aurantimonas manganoxydans, and the importance of getting the concentration right for good level of expression and activity. (DOI 10.1007/s10529-013-1215-5)

Sequential Oxidations of Thiolates and the Cobalt Metallocenter in a Synthetic Metallopeptide: Implications for the Biosynthesis of Nitrile Hydratase

This is a paper in Inorganic Chemistry from the group of Anne K Jones looking at the use of a heptapeptide they call SODA (ACDLPCG) to model the oxidation process for the thiols and metal in the active site of cobalt centre NHases (DOI: 10.1021/ic400171z). First to oxidize is one of the thiolates to sulfinate, then the cobalt is oxidized to triply charged cobalt. Further sulphur oxidation is not observed and the complex is catalytically inactive. This complex does not have an axial thiolate ligand which may explain these last two obervations.

Identification of an active site bound Nitrile Hydratase Intermediate through Single Turnover Stopped-Flow Spectroscopy

This is a paper in the Journal of Biological Chemistry by Natalie Gumataotao, Misty L. Kuhn, Natalia Hajnas and Richard C. Holz (DOI:10.1074/jbc.M112.398909). Using stopped-flow methodology on the NHase from Rhodococcus equi TG328-2, the authors observe evidence of the first Fe3+-nitrile intermediate species ever reported, and hence show the direct ligation of nitrile to metal during catalytic turnover.

Improving stability of nitrile hydratase by bridging the salt-bridges in specific thermal-sensitive regions

This is a paper in Journal of Biotechnology by Jie Chen, Huimin Yu, Changchun Liu, Jie Liu and Zhongyao Shen (doi:10.1016/j.jbiotec.2013.01.021) on methodology to stabilize notoriously temperature sensitive nitrile hydratase. It involves the transfer of three regions which are prone to thermal deformation from thermophilic Bacillus SC-105-1 and Pseudonocardia thermophila JCM3095 into mesophilic Rhodococcus ruber TH.
Three types of salt bridges—active-center-adjacent (in A1), internal neighboring-residue-bridged (in A2) and C-terminal-residue-bridged (A3) were tried but only the type with A3 had increased efficacy at higher temperatures.

A Japanese patent for an "improved nitrile hydratase"

See this or this to see a Japanese patent awarded to Dia-Nitrix Co Ltd, F. Watanabe, T. Ambo and A. Hara, and published on 6th December 2012.



(It is in Japanese)

Self-Subunit Swapping Occurs in Another Gene Type of Cobalt Nitrile Hydratase

Liu Y, Cui W, Xia Y, Cui Y, Kobayashi M, et al. (2012) Self-Subunit Swapping Occurs in Another Gene Type of Cobalt Nitrile Hydratase. PLoS ONE 7(11): e50829. doi:10.1371/journal.pone.0050829.