Recombinant Production and Biochemical Characterization of Thermostable Arabinofuranosidase from Acidothermophilic Alicyclobacillus Acidocaldarius

The complete enzymatic degradation of lignocellulosic biomass requires the cooperative action of cellulosic, hemicellulosic, and lignolytic enzymes such as cellulase, xylanase, laccase, galactosidase, and arabinofuranosidase. Arabinofuranosidases (E.C 3.2.1.55), which belong to the glycoside hydrolase family of enzymes, hydrolyze the 1,3- and 1,5-α-arabinosyl bonds in L-arabinose- containing molecules. L-arabinoses are present in hemicellulosic part of lignocellulosic biomass. Arabinofuranosidases also play an important role in the complete hydrolysis of arabinoxylans. Analysis of the genome project and CAZY database revealed two putative arabinofuranosidase genes in the A. acidocaldarius genome. The aim of the study was cloning, heterologous expression, purification and biochemical characterization of the arabinofuranosidase enzyme encoded in A. acidocaldarius genome. For this purpose, the AbfA gene of the arabinofuranosidase protein was cloned into the pQE-40 vector, heterologously expressed in E. coli BL21 GOLD (DE3) and successfully purified using His-Tag. Biochemical characterization of the purified enzyme revealed that A. acidocaldarius arabinofuranosidase exhibited activity over a wide pH and temperature range with optimum activity at 45 ºC and pH 6.5 in phosphate buffer towards 4-nitrophenyl-α-L-arabinofuranoside as the substrate. In addition, the enzyme is highly stable over wide range of temperature and maintaining 60% of its activity after 90 min of incubation at 80 ºC. Through the bioinformatics studies, the homology model of A. acidocaldarius arabinofuranosidase was generated and the substrate binding site and residues located in this site were identified. Further molecular docking analysis revealed that the substrate located in the catalytically active pose and, residues N174, E175, and E294 have direct interaction with 4-nitrophenyl-α-L-arabinofuranoside. Moreover, based on phylogenetic analysis, A. acidocaldarius arabinofuranosidase exists in the sub-group of intracellular arabinofuranosidases, and G. stearothermophilus and B.subtilis arabinofuranosidases are close relatives of A. acidocaldarius arabinofuranosidase. This is the first study to report the gene cloning, recombinant expression and biochemical and bioinformatic characterization of an auxiliary GH51 arabinofuranosidase from an acidothermophilic bacterium A. acidocaldarius. © 2023, The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature

Mikroorganizmalardan antimikrobiyal peptid üretimi, immobilizasyonu ve uygulamaları

Savunma peptidleri olarak da bilinen antimikrobiyal peptidler (AMP'ler), mikroorganizmalardan insanlara kadar pek çok çeşitli yaşam formları tarafından üretilen kısa ve genel olarak pozitif yüklü peptidlerdir. AMP'lerin çoğu mikrobiyal patojenleri doğrudan öldürme kabiliyetine sahipken, diğerleri konakçı savunma sistemlerini değiştirerek dolaylı olarak etki ederler. Tüm dünyada konvansiyonel antibiyotiklere karşı hızla artan direnç gelişiminin sonucu olarak AMP'leri klinik kullanıma dahil etme çabaları hızlanmaktadır. Bazı AMP'ler şu anda klinik çalışmalarda yeni anti-enfektifler olarak değerlendirilmekte, aynı zamanda bağışıklık tepkisini modüle etmek, yara iyileşmesini hızlandırmak ve ameliyat sonrası yapışmayı önlemek için yeni farmakolojik maddeler olarak kullanım potansiyeli araştırılmaktadır. Bu çalışmada farklı mikroorganizmalardan AMP üretilmesi, üretilen AMP'nin saflaştırılması ve saflaştırılan AMP'nin kalsiyum aljınata immobilize edilerek antimikrobiyal özellikte biyomateryal geliştirilmesi amaçlanmıştır. Bu amaç doğrultusunda Lactobacillus pentosus (DSM 16366), Bacillus subtilis (DSM 347), B. cereus, Pseudomonas aeruginosa (ATCC 27853) ve B. subtilis (ATCC 6653) mikroorganizmalardan AMP üretimi gerçekleştirilmiştir. AMP üretiminin optimizasyonu çalışmaları yapılmıştır. Optimizasyonda karbon kaynağı türü ve miktarı, azot kaynağı türü ve miktarı, pH ve sıcaklık parametreleri incelenmiştir. AMP üretimi her iki saatte bir besi ortamlarından alınan örneklere antibakteriyel test uygulanması ile takip edilmiştir. Antibakeriyel test aşamasında Disk Difüzyon Metodu kullanılmıştır. AMP üretiminin optimizasyonu sonucunda en yüksek antibakteriyel aktivite elde edilen mikroorganizmadan (L. pentosus (DSM 16366)) AMP saflaştırılması gerçekleştirilmiştir. Saflaştırılan AMP kalsiyum aljinat boncuklarına 1-etil-3-(3-dimetilaminopropil)kabodiimid (EDC) kullanılarak kovalent olarak immobilize edilmiştir. Tez çalışması sonucunda geliştirilmesi hedeflenen ürün antibakteriyel olarak tasarlandığından dolayı antibakteriyel teste tabi tutulmuştur. Antibakteriyel test sonucunda, AMP immobilize kalsiyum aljınat boncuğu uygulanan bölgede mikrobiyal üreme gözlenmemiştir. Sonuç olarak mikroorganizmalardan AMP üretimi, üretilen AMP nin saflaştırılması ve uygulama olarak da saflaştırılan AMP'nin kalsiyum aljinat boncuklarına immobilizasyonu başarılı bir şekilde gerçekleştirilmiş ve antibakteriyel özellikte bir biyomateryal elde edilmiştir. Tez çalışması sonucunda elde edilen ürün, aljinatın yara örtüsü olarak kullanım özelliğinden de faydalanılarak özellikle açık yaralarda mikrobiyal kontaminasyonu engellemek amacıyla kullanılma potansiyeline sahiptir.Antimicrobial peptides (AMPs), also known as host defense peptides, are short and generally positively charged peptides found in a wide variety of life forms from microorganisms to humans. Most AMPs have the ability to kill microbial pathogens directly, whereas others act indirectly by modulating the host defense systems. Against a background of rapidly increasing resistance development to conventional antibiotics all over the world, efforts to bring AMPs into clinical use are accelerating. Several AMPs are currently being evaluated in clinical trials as novel anti-infectives, but also as new pharmacological agents to modulate the immune response, promote wound healing, and prevent post-surgical adhesions. In this study, it is aimed that produce and purify AMP from different microorganisms and develop biomaterial with antimicrobial properties via immobilization of purified AMPs to calcium alginate. For this purpose, AMP production from Lactobacillus pentosus (DSM 16366), Bacillus subtilis (DSM 347), B. cereus, Pseudomonas aeruginosa (ATCC 27853) and B. subtilis (ATCC 6653) was performed. Optimization studies of AMP production were carried out. In the optimization studies, carbon source type and amount, nitrogen source type and amount, pH and temperature parameters were examined. AMP production was monitored every two hours by applying antibacterial test to the samples taken from the media. Disc diffusion method was used in the antibacterial test stage. AMP purification was performed from the microorganism (L. pentosus (DSM 16366)) which indicated the highest antibacterial activity as a result of optimization of AMP production. The purified AMP was covalently immobilized to calcium alginate beads using 1-ethyl-3- (3-dimethylaminopropyl) cabodiimide (EDC). As a result of the thesis, the product which was aimed to be developed was subjected to antibacterial test as it was designed as antibacterial. As a result of the antibacterial test, microbial growth was not observed in the region where AMP immobilized calcium alginate bead was applied. As a result, AMP production from microorganisms, purification of the produced AMP and immobilization of purified AMP to calcium alginate beads were achieved successfully and an antibacterial biomaterial was obtained. The product obtained as a result of the thesis has the potential to be used in order to prevent microbial contamination especially in open wounds by taking advantage of the use of alginate as a wound dressing