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All Journal HAYATI Journal of Biosciences Makara Journal of Science Jurnal Bioteknologi & Biosains Indonesia
NIKNIK NURHAYATI
Center for Bioindustrial Technology, Laboratorium of Bioindustrial Technology, LAPTIAB BPPT Puspiptek -Serpong
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Earth & Planetary Sciences

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Sequence-Structure Based Comparison of Structurally Homologous Thermophilic and Mesophilic Polyethylene Terephthalate (PET) Hydrolases Hasan, Khomaini; Ulfah, Maria; Nurhayati, Niknik; Sabbathini, Gabriela Christy; Wulandari, Sri Rezeki; Putra, I Gede Eka Perdana; Helianti, Is
HAYATI Journal of Biosciences Vol. 31 No. 2 (2024): March 2024
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.31.2.348-356

Abstract

Protein structure has a direct impact on thermostability. Deviations in the primary sequence can affect structural changes, leading to alterations in thermostability properties. However, the molecular basis of protein thermostability is unspecified; thus, elucidation of key factors that role particular protein thermostability is required when engineering proteins to be thermostable. To address this challenge, the amino acid composition, hydrophobicity/hydrophilicity ratio, cysteine bridges, and intrinsic features of two structurally homologous but different thermostability, poly(ethylene terephthalate) hydrolase (PETase) were compared. According to the findings, thermostable and thermolabile PETases have similar folds, compactness, and disulfide bridges. Interestingly, an abundance gap of aromaticity, hydrophobic cluster area, polar amino acid and hydrogen bond network compositions demonstrated dominant trends of variations for both PET hydrolases, indicating a pivotal role of these features in the thermostability of PET hydrolase. Furthermore, increased hydrophobic amino acid frequency in the inner surface of thermostable proteins contributed significantly to thermostability by forming more internal hydrophobic interactions and a less hydrophobic patch. There are no consistent trends in insertions and deletions between both PETases. Taken together, these observations demonstrate that hydrophobicity and hydrogen bond networks are essential factors in thermostability of thermostable PETase.
Optimizing the Expression of Polyethylene Terephtalate Hydrolase-Encoding Synthetic Gene in Escherichia coli Arctic Express (DE3) Nataniel, Jocelyn; Ulfah, Maria; Achnafani, Dini; Nurhayati, Niknik; Sabbathini, Gabriela Christy; Wulandari, Sri Rezeki; Abinawanto, Abinawanto; Helianti, Is
Makara Journal of Science Vol. 28, No. 2
Publisher : UI Scholars Hub

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Abstract

The waste of polyethylene terephthalate (PET) plastic waste in Indonesia is a pressing concern due to its slow degradation and potential environmental damage. One promising solution is to utilize polyethylene terephthalate hydrolase from Ideonella sakaiensis (IsPETase), an enzyme that specifically degrades PET. However, inducing the expression of IsPETase synthetic gene in Escherichia coli BL21 (DE3) has been challenging because much of it remains insoluble. This study aimed to express IsPETase in E. coli Arctic Express (DE3) and optimize the conditions to enhance its production. First, pET22b(+)pelB-IsPETase was inserted into E. coli Arctic Express (DE3). The recombinant E. coli Arctic Express (DE3) was induced with isopropyl-β-D-1-thiogalactopyranoside (IPTG) and incubated at 10 °C. The fraction expressing soluble IsPETase was determined in different culture media, IPTG concentrations, induction times, and soni-cation durations. Parameters were optimized using a one-factor-at-a-time approach and then evaluated based on esterase specific activity and SDS-PAGE analysis. Results showed that IsPETase can be expressed in extracellular, periplasmic, and cytoplasmic soluble fractions. However, the extracellular fraction should be concentrated. Subsequent optimization focused only on the cytoplasmic fraction under optimal conditions, achieving a threefold increase in PETase specific activity compared with that under uninduced IPTG conditions. The reaction of PETase enzyme with PET and PCL was proven by weight loss, Scanning electron microscope (SEM), and Fourier transform infrared spectroscopy (FTIR). Although successful IsPETase expression and production optimization have been achieved, the specific activity remains low, prompting the need for ongoing expression optimization.
Screening for Penicillin G Acylase (PGA)-Producing Bacteria and Gene Cloning Using Degenerate Oligonucleotide Primed-PCR Masdalifah, Masdalifah; Wulandari, Sri Rezeki; Sabbathini, Gabriela Christy; Ulfah, Maria; Achnafani, Dini; Wibisana, Ahmad; Sriherfyna, Feronika Heppy; Helianti, Is; Nurhayati, Niknik
Makara Journal of Science Vol. 29, No. 1
Publisher : UI Scholars Hub

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Abstract

The growing concern over antibiotic resistance has driven global efforts to explore innovative solutions, including the use of Penicillin G acylase (PGA) to produce semisynthetic β-lactam antibiotics. This study screened four potential in-tracellular PGA-producing bacteria: Alcaligenes faecalis InaCC B444 (AfPGA), Kluyvera cryocrescens InaCC B850 (KcPGA), Providencia rettgeri InaCC B25 (Pr25PGA), and P. rettgeri InaCC B466 (Pr466PGA). Penicillin G Acylase encoding genes (pgas) were isolated from them using a Degenerate Oligonucleotide Primed-PCR (DOP-PCR) approach and sequenced. Microbiological assays confirmed all tested crude extracts to exhibit inhibitory effects. Penicillin G was used for evaluating hydrolytic activity and 6-Amino Penicillanic Acid (6-APA) coupled with D-p-Hydroxyl-phenylglycine methyl ester hydrochloride (DHPGME) for the synthetic activity. Pr466PGA and Pr25PGA showed the highest synthetic and hydrolytic activities, respectively. DOP-PCR successfully amplified a 2,517 bp pga-encoding Pr25PGA. The deduced amino acid sequence shared 95.1% identity with the known PGA from P. rettgeri PX04. Sec-ondary structure analysis of Pr25PGA revealed 35% α-helices, 16% β-sheets, and 49% coils, suggesting that the enzyme may be flexible and dynamic, with structural stability primarily provided by the α-helices and β-sheets. These findings offer valuable insights for the future design and application of Pr25PGA, particularly in the production of semisynthetic β-lactam antibiotics.
ENZYMATIC DEGUMMING USING XYLANASE AND PECTINASE TO IMPROVE BRIGHTNESS AND FINENESS QUALITY OF RAMIE FIBER (Boehmeria nivea L.) AS TEXTILE RAW MATERIAL Abidin, Kharis Yohan; Nurhayati, Niknik; Nandyawati, Dewi; Sabbathini , Gabriela Christy
Jurnal Bioteknologi & Biosains Indonesia (JBBI) Vol. 10 No. 1 (2023)
Publisher : BRIN - Badan Riset dan Inovasi Nasional

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.55981/jbbi.2023.1744

Abstract

Ramie (Boehmeria nivea L.) fiber is an alternative to cotton fiber, and the degumming process is crucial for preparing it as a textile raw material. This study investigates the enzymatic degumming of ramie fiber using a combination of xylanase enzyme from Bacillus halodurans CM1 and commercial pectinase enzyme. The objective is to assess the impact of enzymatic degumming on the physical properties (weight loss, whiteness index, tenacity, elongation, and fineness) of ramie fiber. The degumming process was conducted in a shaker incubator at a temperature of 50 °C, pH 9, and 150 rpm. The degumming treatment involved 3% v/v xylanase, 1% v/v pectinase, 1% v/v surfactant, and 0.05% v/v NaClO2. The results show that the bleaching treatment (S6) resulted in higher fiber weight loss (9.52%), whiteness index (87.87%), tenacity (20.08 g/Tex), and fineness (1.05 denier) compared to the non-bleaching treatment.
Co-Authors Abinawanto Abinawanto Achnafani, Dini Ahmad Wibisana, Ahmad Feronika Heppy Sriherfyna I Gede Eka Perdana Putra, I Gede Eka Perdana IS HELIANTI Kharis Yohan Abidin, Kharis Yohan KHOMAINI HASAN Maria Ulfah Masdalifah, Masdalifah NANDYAWATI, DEWI Nataniel, Jocelyn Sabbathini , Gabriela Christy Sabbathini, Gabriela Christy Wulandari, Sri Rezeki