Nylon-eating bacteria

File:6-Aminocaproic acid.png]]

In 1975, a team of Japanese scientists discovered a strain of bacterium, living in ponds containing waste water from a nylon factory, that could digest certain byproducts of nylon 6 manufacture, such as the linear dimer of 6-aminohexanoate. These substances are not known to have existed before the invention of nylon in 1935. It was initially named as Achromobacter guttatus.{{cite journal | author = Kinoshita, S. |author2=Kageyama, S. |author3=Iba, K. |author4=Yamada, Y. |author5=Okada, H. |title=Utilization of a cyclic dimer and linear oligomers of e-aminocaproic acid by Achromobacter guttatus KI 72 |journal=Agricultural and Biological Chemistry |volume=39 |issue=6 |pages=1219–23 |year=1975 |issn=0002-1369 |doi=10.1271/bbb1961.39.1219|doi-access=free }}

Studies in 1977 revealed that the three enzymes that the bacteria were using to digest the byproducts were significantly different from any other enzymes produced by any other bacteria, and not effective on any material other than the manmade nylon byproducts.{{Cite journal|title=6-Aminohexanoic Acid Cyclic Dimer Hydrolase. A New Cyclic Amide Hydrolase Produced by Achromobacter Guttatus KI74|last1=S|first1=Kinoshita|last2=S|first2=Negoro|date=1977-11-01|journal=European Journal of Biochemistry|language=en|pmid=923591|last3=M|first3=Muramatsu|last4=Vs|first4=Bisaria|last5=S|first5=Sawada|last6=H|first6=Okada|volume=80|issue=2|pages=489–95|doi=10.1111/j.1432-1033.1977.tb11904.x}}

The bacterium was reassigned to Flavobacterium in 1980.{{cite journal |last1=Negoro |first1=S |last2=Shinagawa |first2=H |last3=Nakata |first3=A |last4=Kinoshita |first4=S |last5=Hatozaki |first5=T |last6=Okada |first6=H |title=Plasmid control of 6-aminohexanoic acid cyclic dimer degradation enzymes of Flavobacterium sp. KI72. |journal=Journal of Bacteriology |date=July 1980 |volume=143 |issue=1 |pages=238–45 |doi=10.1128/JB.143.1.238-245.1980 |pmid=7400094 |pmc=294219 |doi-access=free}} Its genome was resolved in 2017, again reassigning it to Arthrobacter. The Genome Taxonomy Database considers it a strain of Paenarthrobacter ureafaciens following a 2016 reclassification.{{cite web |title=GTDB - GCF_002049485.1 |url=https://gtdb.ecogenomic.org/genomes?gid=GCF_002049485.1 |website=Genome Taxonomy Database, revision 95|date=2020}} As of January 2021, the NCBI taxonomy browser has been updated to match GTDB.

A few newer strains have been created by growing the original KI72 in different conditions, forcing it to adapt. These include KI722, KI723, KI723T1, KI725, KI725R, and many more.{{cite journal |last1=Negoro |first1=S |last2=Kakudo |first2=S |last3=Urabe |first3=I |last4=Okada |first4=H |title=A new nylon oligomer degradation gene (nylC) on plasmid pOAD2 from a Flavobacterium sp. |journal=Journal of Bacteriology |date=1992 |volume=174 |issue=24 |pages=7948–7953 |doi=10.1128/jb.174.24.7948-7953.1992|pmid=1459943 |pmc=207530 |doi-access=free }}

The bacterium contains the following three enzymes:

• 6-aminohexanoate-cyclic-dimer hydrolase (EI, NylA, {{UniProt|P13398}})
• 6-aminohexanoate-dimer hydrolase (EII, NylB, {{UniProt|P07061}})
• 6-aminohexanoate-oligomer endohydrolase (EIII, NylC, {{UniProt|Q57326}})

All three enzymes are encoded on a plasmid called pOAD2. The plasmid can be transferred to E. coli, as shown in a 1983 publication.

{{cite journal

|vauthors= Negoro S, Taniguchi T, Kanaoka M, Kimura H, Okada H

|title= Plasmid-determined enzymatic degradation of nylon oligomers

|journal= J. Bacteriol. |volume= 155 |issue= 1 |pages= 22–31

|date= July 1983 |doi= 10.1128/JB.155.1.22-31.1983

|pmid= 6305910 |pmc= 217646

|url= }}

The enzyme EI is related to amidases. Its structure was resolved in 2010.{{cite journal |last1=Yasuhira |first1=K |last2=Shibata |first2=N |last3=Mongami |first3=G |last4=Uedo |first4=Y |last5=Atsumi |first5=Y |last6=Kawashima |first6=Y |last7=Hibino |first7=A |last8=Tanaka |first8=Y |last9=Lee |first9=YH |last10=Kato |first10=D |last11=Takeo |first11=M |last12=Higuchi |first12=Y |last13=Negoro |first13=S |title=X-ray crystallographic analysis of the 6-aminohexanoate cyclic dimer hydrolase: catalytic mechanism and evolution of an enzyme responsible for nylon-6 byproduct degradation. |journal=The Journal of Biological Chemistry |date=8 January 2010 |volume=285 |issue=2 |pages=1239–48 |doi=10.1074/jbc.M109.041285 |pmid=19889645 |pmc=2801252 |doi-access=free}}

EII has evolved by gene duplication followed by base substitution of another protein EII'. Both enzymes have 345 identical aminoacids out of 392 aminoacids (88% homology). The enzymes are similar to beta-lactamase.{{Cite journal|last1=Okada|first1=H.|last2=Negoro|first2=S.|last3=Kimura|first3=H.|last4=Nakamura|first4=S.|date=10–16 November 1983|title=Evolutionary adaptation of plasmid-encoded enzymes for degrading nylon oligomers|journal=Nature|volume=306|issue=5939|pages=203–206|doi=10.1038/306203a0|issn=0028-0836|pmid=6646204|bibcode=1983Natur.306..203O|s2cid=4364682}}

The EII' (NylB', {{UniProt|P07062}}) protein is about 100x times less efficient compared to EII. A 2007 research by the Seiji Negoro team shows that just two amino-acid alterations to EII', i.e. G181D and H266N, raises its activity to 85% of EII.{{cite journal |vauthors= Negoro S, Ohki T, Shibata N, etal |title= Nylon-oligomer degrading enzyme/substrate complex: catalytic mechanism of 6-aminohexanoate-dimer hydrolase |journal= J. Mol. Biol. |volume= 370 |issue= 1 |pages= 142–56 |date= June 2007 |pmid= 17512009 |doi= 10.1016/j.jmb.2007.04.043 }}

The structure of EIII was resolved in 2018. Instead of being a completely novel enzyme, it appears to be a member of the N-terminal nucleophile (N-tn) hydrolase family.{{cite journal |last1=Negoro |first1=S |last2=Shibata |first2=N |last3=Lee |first3=YH |last4=Takehara |first4=I |last5=Kinugasa |first5=R |last6=Nagai |first6=K |last7=Tanaka |first7=Y |last8=Kato |first8=DI |last9=Takeo |first9=M |last10=Goto |first10=Y |last11=Higuchi |first11=Y |title=Structural basis of the correct subunit assembly, aggregation, and intracellular degradation of nylon hydrolase. |journal=Scientific Reports |date=27 June 2018 |volume=8 |issue=1 |pages=9725 |doi=10.1038/s41598-018-27860-w |pmid=29950566|pmc=6021441 |bibcode=2018NatSR...8.9725N |doi-access=free }} Specifically, computational approaches classify it as a MEROPS S58 (now renamed P1) hydrolase. The protein is expressed as a precursor, which then cleaves itself into two chains.{{cite web |title=Q57326 |url=https://www.ebi.ac.uk/interpro/protein/UniProt/Q57326/ |website=InterPro}}{{Cite web|url=https://www.ebi.ac.uk/merops/cgi-bin/pepsum?id=P01.102|title=MEROPS - the Peptidase Database}} Outside of this plasmid, > 95% similar proteins are found in Agromyces and Kocuria. As of 2025, 9 homologues of NylC are described from different Actinobacteria (Plastic Enzyme Database PAZY., accessed 12.02.2025).{{cite web |title=PAZY |url=https://www.pazy.eu/doku.php?id=pa |website=PAZY}}

EIII was originally thought to be completely novel. Susumu Ohno proposed that it had come about from the combination of a gene-duplication event with a frameshift mutation. An insertion of thymidine would turn an arginine-rich 427aa protein into this 392aa enzyme.{{cite journal |author= Ohno S |title= Birth of a unique enzyme from an alternative reading frame of the preexisted, internally repetitious coding sequence |journal= Proc Natl Acad Sci USA |volume= 81 |issue= 8 |pages= 2421–5 |date= April 1984 |pmid= 6585807 |pmc= 345072 |doi= 10.1073/pnas.81.8.2421|bibcode= 1984PNAS...81.2421O |doi-access= free }}

{{main|Nylon-eating bacteria and creationism}}

There is scientific consensus that the capacity to synthesize nylonase most probably developed as a single-step mutation that survived because it improved the fitness of the bacteria possessing the mutation. More importantly, one of the enzymes involved was produced by a frame-shift mutation that completely scrambled existing genetic code data.{{Cite journal |last=Ohno |first=S |date=April 1984 |title=Birth of a unique enzyme from an alternative reading frame of the preexisted, internally repetitious coding sequence. |journal=Proceedings of the National Academy of Sciences |language=en |volume=81 |issue=8 |pages=2421–2425 |doi=10.1073/pnas.81.8.2421 |doi-access=free |issn=0027-8424 |pmc=345072 |pmid=6585807|bibcode=1984PNAS...81.2421O }} Despite this, the new gene still had a novel, albeit weak, catalytic capacity. This is seen as a good example of how mutations easily can provide the raw material for evolution by natural selection.{{cite journal |author=Thwaites WM |title=New Proteins Without God's Help |journal=Creation Evolution Journal |volume=5 |issue=2 |pages=1–3 |date=Summer 1985 |url=http://ncse.com/cej/5/2/new-proteins-without-gods-help}}{{cite web |date= |title=Evolution and Information: The Nylon Bug |url=http://www.nmsr.org/nylon.htm |access-date=2023-09-27 |publisher=New Mexicans for Science Education}}{{Cite web |last=Than |first=Ker |date=2005-09-23 |title=Why scientists dismiss 'intelligent design' |url=https://www.nbcnews.com/id/wbna9452500 |access-date=2023-09-27 |website=NBC News |language=en}}Miller, Kenneth R. Only a Theory: Evolution and the Battle for America's Soul (2008) pp. 80-82

A 1995 paper showed that scientists have also been able to induce another species of bacterium, Pseudomonas aeruginosa, to evolve the capability to break down the same nylon byproducts in a laboratory by forcing them to live in an environment with no other source of nutrients.{{cite journal|vauthors=Prijambada ID, Negoro S, Yomo T, Urabe I|date=May 1995|title=Emergence of nylon oligomer degradation enzymes in Pseudomonas aeruginosa PAO through experimental evolution|url= |journal=Appl. Environ. Microbiol.|volume=61|issue=5|pages=2020–2|doi=10.1128/AEM.61.5.2020-2022.1995|pmc=167468|pmid=7646041|bibcode=1995ApEnM..61.2020P}}

Integration of EI and EII into the genome of the bacterium Pseudomonas putida KT2440 enabled the development of a strain that can metabolize Nylon oligomers.{{cite journal |last=de Witt |first=J |last2=Luthe |first2=T |last3=Wiechert |first3=J |last4=Jensen |first4=K |last5=Polen |first5=T |last6=Wirtz |first6=A |last7=Thies |first7=S |last8=Frunzke |first8=J |last9=Wynands |first9=B |last10=Wierckx |first10=N |title=Upcycling of polyamides through chemical hydrolysis and engineered Pseudomonas putida. |journal=Nature Microbiology |volume=2025 |issue=10 |pages=667–680 |year=2025 |doi=10.1038/s41564-025-01929-5|doi-access=free|pmc=11879879 }} Metabolism of common Nylon monomers like aminocaproic acid and hexamethylenediamine was realised by the deregulation of polyamine metabolism, guided by Adaptive laboratory evolution experiments with nylon components as sole source of nutrients. The adipic acid resulting from this metabolic pathway feeds into the central metabolism via a specialized beta oxidation pathway obtained from Acinetobacter baylyi.{{cite journal |last=Ackermann |first=Y |last2=Li |first2=W-J |last3=Op de Hipt |first3=L |last4= Niehoff |first4=P-J |last5=Casey |first5=W |last6=Polen |first6=T |last7=Koebbing |first7=S|last8=Ballerstedt |first8=H |last9=Wynands |first9=B |last10=O'Connor |first10=K |last11=Blank |first11=LM |last12=Wierckx |first12=N |title=Engineering adipic acid metabolism in Pseudomonas putida. |journal=Metabolic Engineering |volume=67 |pages=29–40 |year=2021 |doi=10.1016/j.ymben.2021.05.001|doi-access=free}}

• Plastivore
• Biodegradable plastic
• E. coli long-term evolution experiment
• Radiotrophic fungus
• London Underground mosquito
• Lonicera fly
• Mealworms are capable of digesting polystyrene

{{Reflist|2}}

• {{cite journal |vauthors=Yomo T, Urabe I, Okada H |title=No stop codons in the antisense strands of the genes for nylon oligomer degradation |journal=Proc Natl Acad Sci USA |volume=89 |issue=9 |pages=3780–4 |date=May 1992 |pmid=1570296 |pmc=525574 |doi=10.1073/pnas.89.9.3780|bibcode=1992PNAS...89.3780Y |doi-access=free }}

• [https://www.nite.go.jp/nbrc/catalogue/NBRCCatalogueDetailServlet?ID=NBRC&CAT=00014590 NBRC 14590], information on the KI72 culture maintained at National Institute of Technology and Evaluation
• [https://www.nite.go.jp/nbrc/catalogue/NBRCCatalogueDetailServlet?ID=NBRC&CAT=00114184 NBRC 114184], a derived culture used in the 2017 sequencing
• {{GO|GO:0019876|label=Nylon catabolic process}}

{{Taxonbar|from=Q4353307}}

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Category:Biological evolution

Category:Plastivores

Category:Actinomycetota