Svet se že vrsto let bori proti veliki uporabi plastike in za trajnostno upravljanje z odpadki. Vse bolj vznika področje razgradnje plastike ob pomoči mikroorganizmov. V
naši raziskavi smo želeli preko znanih proteinskih sekvenc, ki imajo eksperimentalno potrjeno vlogo v razgradnji plastike, iskati podobne encime. Kljub nestandardiziranemu
poročanju raziskovalnih skupin na področju razgrajevanja plastike, smo uspešno pregledali več kot 400 znanstvenih člankov in zbrali podatke o 516 edinstvenih
mikroorganizmih, ki so bili predmet raziskav o razgradnji plastike. Podatkovna zbirka vsebuje podatke o razgradnji 14 polimerov. Z uporabo analiz MAFFT in CD-HIT smo
identificirali 385 skupin, iz katerih smo izbrali 11 gruč z največjim številom encimskih sekvenc za nadaljnje raziskave. Iz vsake skupine smo izbrali tri taksonomsko raznolike
organizme. Za nadaljnjo analizo smo uporabili proteinske sekvence FASTA, ki so nam služile kot osnova za identifikacijo potencialnih kandidatnih organizmov, sposobnih razgraditi plastične polimere. Opazili smo izrazito prevlado hidrolaz. Za vsako skupino
smo sestavili filogenetska drevesa, ki so vodila nadaljnje analize, namenjene identifikaciji novih mikroorganizmov morda zanimivih za biološko razgradnjo plastike.
Poleg tega smo izvedli analizo encimskih domen z uporabo InterProScan in HMMER 3.4. Nazadnje smo začetne mikroorganizme razvrstili v podatkovno zbirko, v kateri smo
identificirali 598 organizmov. Razvrstili smo jih po lestvici od 1 (najmanj zanesljivo) do 3 (najbolj zanesljivo), glede na stopnjo zaupanja, s katero lahko trdimo, da je določeno proteinsko zaporedje povezano z razgradnjo plastike. Podatkovno zbirko smo
nato objavili na spletnem portalu GitHub na (
https://github.com/SergejB-BF/plasticdegrading-enzymes-database).
| Language: | English |
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| Title: | Development of a database of genes encoding enzymes for degradation of plastic polymers |
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| Abstract: |
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For many years, the world has been fighting against the widespread use of plastic and for sustainable plastic waste management. The field of plastic degradation with the help
of microorganisms is becoming increasingly popular. In our research, we wanted to search for similar enzymes using known protein sequences that have an experimentally
confirmed role in plastic degradation. Despite the non-standardized reporting of research groups in the field of plastic degradation, we successfully reviewed more than
400 scientific articles and collected data on 516 unique microorganisms that have been the subject of plastic degradation research. The database contains data on the
degradation of 14 polymers. Using MAFFT and CD-HIT analyses, we identified 385 groups, from which we selected 11 clusters with the highest number of enzyme sequences for further research. From each group, we selected three taxonomically
diverse organisms. For further analysis, we used FASTA protein sequences, which served as the basis for identifying potential candidate organisms capable of degrading
plastic polymers. We observed a marked predominance of hydrolases. For each group, we constructed phylogenetic trees that guided further analyses aimed at identifying new
microorganisms that may be of interest for the biodegradation of plastics. In addition, we performed an analysis of enzyme domains using InterProScan and HMMER 3.4.
Finally, we classified the initial microorganisms into a database in which we identified 598 organisms. We classified them on a scale from 1 (least reliable) to 3 (most reliable), depending on the degree of confidence with which we can claim that a particular protein sequence is related to plastic degradation. We published the database on the GitHub web portal at ( https://github.com/SergejB-BF/plastic-degrading-enzymes-database).
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| Keywords: | enzymes plastics degradation functional domains PETase bioinformatics database |
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