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All Journal HAYATI Journal of Biosciences Bioma : Berkala Ilmiah Biologi Indonesian Journal of Biotechnology Berkala Bioteknologi Makara Journal of Science
IS HELIANTI
Center for Bioindustrial Technology, Laboratorium of Bioindustrial Technology, LAPTIAB BPPT Puspiptek -Serpong
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Earth & Planetary Sciences Education Immunology & microbiology Materials Science & Nanotechnology

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Kloning dan Sekuensing Gen Xilanase dengan Produk Gen Berukuran 30 kDa dari Bacillus halodurans CM1 pada Escherichia coli DH5α Safirah, Dearesty; Helianti, Is; Kusumaningrum, Hermin Pancasakti; Budiharjo, Anto
Bioma : Berkala Ilmiah Biologi Vol. 18, No.2, Tahun 2016
Publisher : Departemen Biologi, Fakultas Sains dan Matematika, Universitas Diponegoro

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (98.71 KB) | DOI: 10.14710/bioma.18.2.167-172

Abstract

The paper industry contributed the environment pollution due to chlor substances. Utilization of alkalothermophilic xylanase enzyme as a biocatalyst in the production of paper may become an environmentally friendly biobleaching alternative. Bacillus halodurans CM1 produces xilanase enzyme that had optimal activity at pH 9 and temperature 70°C. Previous study showed that this CM1 strains has several xilanase genes. The cloning of one of these alkalothermophiic xylanase (alkxyn) gene has been already conducted. This study aimed to clone alkxyn gene that encode alkalothermophilic xylanase enzyme from B. halodurans CM1 into Escherichia coli DH5α. Amplification of alkxyn has been carried out using primers for amplification xylanase 30 kDa. The alkxyn gene fragment was inserted into pGEM-T Easy vector and then transformed into E. coli DH5α. The results showed that the recombinant of E. coli DH5α harboring alkxyn gene from B. halodurans CM1 has been obtained. The sequences analysist based on BLAST showed that alkxyn fragment has homology (99%) with the alkaliphilic xylanase gene from Bacillus sp. 31 which encodes alkaliphilic xilanase (Genebank assession number: JF912895.1). Keywords: cloning, Bacillus halodurans CM1, xylanase, alkalothermophilic.
Cloning of a Gene Encoding Protease from Bacillus halodurans CM1 into Escherichia coli DH5α and Expression Analyses of the Gene Product Helianti, Is; Furgeva, Natasha; Mulyawati, Lina; Ferniah, Rejeki Siti; Kusumaningrum, Hermin Pancasakti
Makara Journal of Science Vol. 22, No. 3
Publisher : UI Scholars Hub

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Abstract

Bacillus halodurans strain CM1 is an Indonesia alkalothermophilic bacterium isolated from Cimanggu Hot Spring, Bandung, West Java. This bacterial strain produces high levels of thermoalkalophilic xylanase. It has also been predicted to produce other potential industrial enzymes, including protease. For production and application of protease in the future, the protease gene from B. halodurans CM1 was cloned into Escherichia coli. The protease gene was isolated from B. halodurans CM1 by the PCR approach using primers designed based on the GenBank. The PCR product was then ligated into pGEM-T Easy vector, transformed into E. coli DH5α, verified, and analyzed based on DNA sequencing data using the BLAST search tool. A 1086-bp protease gene was obtained that exhibited a very high sequence similarity (99%) with that of alkaline protease gene from B. halodurans C-125. When the culture of this positive recombinant E. coli DH5α containing the protease gene was spotted onto calcium caseinate agar, a clear zone appeared after incubation at 50 °C. This result demonstrated that the protease gene was expressed in this recombinant E. coli DH5α.
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.
The Potential of Bacillus altitudinis B538 and Alcaligenes faecalis B947 in PET and PCL Plastic Degradation Dini, Muthia Rahmah; Nurcholis, Mochamad; Ulfah, Maria; Sabbathini, Gabriela Christy; Wulandari, Sri Rezeki; Helianti, Is
HAYATI Journal of Biosciences Vol. 31 No. 4 (2024): July 2024
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.31.4.621-629

Abstract

Polyethylene terephthalate (PET) plastic is the most widely used type of plastic that produces waste and causes various environmental and health problems. The treatment of PET plastic waste with chemically and mechanically recycling approaches still has shortcomings, so biological processing using microorganisms or enzymes has new potential. Two bacterial isolates from the Indonesian Culture Collection of National Research and Innovation Agency (InaCC, BRIN), namely isolate InaCC B538 and InaCC B947, were further observed for their potential in PET plastic degradation. Firstly, both isolates were determined by the molecular marker 16S rDNA. The potential of both isolates was measured with following method: 10 days of degradation using PET and PCL substrates, esterase enzyme activity assay, and observation of the PET plastic surface using Scanning Electron Microscope (SEM). Species identification was performed using DNA sequencing of 16S rDNA. InaCC B538 and InaCC B947 were closely related to Bacillus altitudinis TBMAX41 and Alcaligenes faecalis AN-13, respectively. InaCC B947 isolate has a better potential in degrading PET plastic and PCL with a degradation percentage of 0.32% for PET plastic and 3.22% for PCL film for 10 days, respectively, and esterase activity of 0.06 U/ml; while InaCC B538 did not cause weight loss of PET and 2.49% for PCL, respectively, with esterase activity of 0.04 U/ml. The degradation of PET plastic by the isolates InaCC B947 was able to cause damage to the plastic surface leading to the degradation of PET plastic.
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.
Overexpression and purification of YidRv gene from the hypervirulent Klebsiella pneumoniae, and the ability of the gene product in inducing a humoral response Raras, Tri Yudani Mardining; Ajrullah, Mauludy Jutta; Gunawan, Ellen Fenix; Pramesti, Nadya Shafa; Prawiro, Sumarno Reto; Wardani, Agustin Krisna; Helianti, Is
Indonesian Journal of Biotechnology Vol 29, No 4 (2024)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.95222

Abstract

The yidRv gene, isolated from the hypervirulent Klebsiella pneumoniae (hvKP), is a novel gene with an unknown function; however, it has exhibited high homology to the yidR, a gene recognized as potential vaccine candidate. The aim of this study was to clone the yidRv gene from the Indonesian hvKP and to investigate its overexpression in Escherichia coli. In the experiment, yidRv was cloned into pET21 to construct pYik23. Recombinant protein YidRv was produced by growing E. coli BL21 (DE3)/pYik23 in LB medium with ampicillin at 29 °C, inducing protein synthesis with 0.5 mM IPTG for 20 hours. Purification was performed using Ni‐NTA resin, and the purified protein (50 µg) was administered to BALB/c mice to test for the production of IgG, IgM and IgA on 2 days before and day 19th and 37th after the first vaccination. The results show a significant induction of IgG and IgM, but not of IgA antibodies. In conclusion, the yidRv gene was overexpressed in E. coli BL21 (DE3) at high levels in soluble form, with the recombinant protein able to be purified to 90% homogeneity. The recombinant YidRv demonstrated the ability to stimulate the generation of both IgM and IgG antibodies.
In Silico and In Vitro Inhibitory Activity of Indonesian Herbal Compound Extracts against SARS-COV-2 Recombinant Papain-Like Protease Fatiningtyas, Fairuz Andini; Napitupulu, Riswanto; Malik, Amarila; Helianti, Is
HAYATI Journal of Biosciences Vol. 32 No. 2 (2025): March 2025
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.32.2.356-366

Abstract

The SARS-CoV-2 papain-like protease (PLpro) is essential for viral replication and a promising target for drug discovery. This study explored the inhibitory potential of compounds from Indonesia herbals Butterfly pea flower (Clitoria ternatea L), Star fruit leaves (Averrhoa carambola L.), and Java plum leaves (Syzygium cumini (L.) Skeels) against PL pro through molecular docking and in vitro assays. The molecular docking method utilized the target protein PLpro (PDB ID: 7CMD), with the native ligand obtained from compounds identified in these plant extracts. The compounds were identified using the KNApSAcK database and analyzed for drug-likeness based on Lipinski's Rule of Five. The physicochemical characteristics affecting absorption, distribution, metabolism, excretion, and toxicity (ADMET) were determined using the pkCSM descriptor algorithm protocol. Validation was performed using the redocking method, achieving an RMSD score of 0.728 Å, which indicated validity (RMSD <2.0 Å). The results identified four ligands with the lowest binding affinities from these extracts: (-)-Epicatechin 3-O-gallate, folic acid, petunidin 3-glucoside, and ellagic acid, with binding scores of -8.6, -8.3, -7.1, and -7.1 kcal/mol, respectively. Prior to conducting the PLpro in vitro inhibition assay, a fluorescence-based inhibition assay was performed using Z-RLRGG-AMC as the substrate and GRL0617as the control inhibitor. All extracts were subjected to 70% ethanol maceration. The IC50 value of GRL0617 was 3.38 μM, while fluorescence tests showed that Java plum leaf extract exhibited the highest inhibition percentage at 66.10±3.22%. These findings indicate that all three plant extracts contain compounds capable of inhibiting PLpro activity.
Cloning of A Gene Encoding Protease from Bacillus halodurans CM1 into Escherichia coli DH5α Furgeva, Natasha; Helianti, Is; Ferniah, Rejeki Siti; K, Hermin Pancasakti
Berkala Bioteknologi Vol. 4, No. 2, November 2021
Publisher : Berkala Bioteknologi

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Abstract

Bacillus halodurans strain CM1 was an Indonesia alkalothermophilic bacteria isolated from Cimanggu Hot Spring, Bandung, West Java. The activity of alkalo thermophilic protease enzyme from B. halodurans CM1 was detected. Nowadays, alkalothermophilic protease enzyme was applied for the eco-friendly industrial purpose, for example, as additive substance in detergent product. For the production and application of protease in the future, the cloning of protease gene from B. halodurans CM1 into E. coli was conducted. The protease gene was isolated from B. halodurans by PCR approach using primers designed based on the GenBank database. The PCR product then ligated into pGEM-T Easy vector, transformed into Escherichia coli DH5α, verified, and analyzed using DNA sequencing and bioinformatic tools BLAST. The results showed that 1086 bp protease gene was obtained and had 99% similarity with that of alkalostable protease from B. halodurans C-125. When the culture of this positive recombinant E. coli DH5α containing the protease gene spotted onto calcium caseinate agar, the clear zone appeared after incubation at 50 °C. It showed that the protease gene was expressed in this recombinant E.coli DH5α.
Co-Authors Abinawanto Abinawanto Achnafani, Dini AGUSTIN KRISNA WARDANI Ajrullah, Mauludy Jutta Amarila Malik Anto Budiharjo Dini, Muthia Rahmah Fatiningtyas, Fairuz Andini Furgeva, Natasha Gunawan, Ellen Fenix Hermin Pancasakti Kusumaningrum I Gede Eka Perdana Putra, I Gede Eka Perdana K, Hermin Pancasakti KHOMAINI HASAN Maria Ulfah Mochamad Nurcholis Mulyawati, Lina Napitupulu, Riswanto Nataniel, Jocelyn NIKNIK NURHAYATI Pramesti, Nadya Shafa Prawiro, Sumarno Reto Rejeki Siti Ferniah Sabbathini, Gabriela Christy Safirah, Dearesty Tri Yudani MR Wulandari, Sri Rezeki