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Characteristics of Nitrogen-Fixing Bacteria Isolated from the Rhizosphere at Kaolin Lake, Belitung, Indonesia Nurhakiki; Rusmana, Iman; Astuti, Rika Indri
HAYATI Journal of Biosciences Vol. 32 No. 3 (2025): May 2025
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.32.3.611-622

Former kaolin mining has poor physical and chemical properties for plants. The low nutrient content makes difficult for plants to grow. Nitrogen (N2) is an important macronutrient for plants, but it can only be absorbed in the form of ammonium ions (NH4+) or nitrate ions (NO3-). Therefore, it is necessary to transform nitrogen, which is able to change the molecular form so that it can be absorbed by plants. The strategy that can be done is using nitrogen-fixing bacteria. This study aimed to explore and analyze the diversity of nitrogen-fixing bacteria based on 16S rRNA and nifH gene from the rhizosphere of the Kaolin Lake area. The method started with bacterial isolation from rhizosphere soil samples. Selected isolates were tested for ammonium content to determine the ability of isolates to fix nitrogen. In this study, 13 isolates had the ability to fix nitrogen, two of which had a high ammonium concentration, namely RBN 5.6, and RBA 2.3. The highest ammonium concentration was produced by isolate RBN5.6 amounting to 7.55 μg/ml. Based on 16S rRNA gene identification, isolate RBN5.6 was similar to Burkholderia cepacia and isolate RBA2.3 was similar to Bacillus aquimaris. Based on the detection of the nifH gene, isolate RBN5.6 was identified as a protein-encoding dinitrogenase reductase gene group cluster from the Stutzerimonas stutzeri.

Influence of Co-feeding Methanol-sorbitol Ratio on Production of Human Insulin Precursor Expressed by Mut+ Pichia pastoris Puspitasari, Dian Japany; Mahsunah, Anis Herliyati; Nurdiani, Dini; Astuti, Rika Indri; Meryandini, Anja
HAYATI Journal of Biosciences Vol. 32 No. 3 (2025): May 2025
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.32.3.581-588

An increasing number of diabetic patients and the demand for insulin encourage the development of recombinant insulin production on a large scale. Human insulin precursor (HIP) expressed by Mut+ Pichia pastoris using methanol as an inducer was developed. However, methanol above 5% (w/v) or 1.56 M is toxic for the host. Sorbitol was introduced as a co-substrate with methanol. To our knowledge, the study of methanol/sorbitol co-feeding on human insulin precursor (HIP) expression by Mut+ Pichia pastoris in a bioreactor has yet to be reported. This study aimed to investigate the influence of the methanol-sorbitol co-feeding ratio on the expression of HIP expressed by P. pastoris X33 Mut+. The study was conducted by comparing the cultivation of P. pastoris/pD902-IP Mut+ in a 10-liter bioreactor under three conditions: feeding 100% methanol, mass ratio of MeOH:sorbitol 12:1 and 3:1. The oxygen consumption of methanol/sorbitol is less than the methanol feeding. The mass ratio of MeOH:sorbitol 12:1 produced the highest HIP titer (1326.5 mg/L), 1.5 times higher than methanol feeding, the lowest specific growth rate, but the highest specific productivity at the induction phase. MeOH:sorbitol mass ratio 3:1 produced the highest dry cell weight (DCW) amount (96 g/L). These results suggested that an appropriate ratio of sorbitol-methanol can be a choice to replace methanol feeding in a Mut+ P. pastoris.

Interaksi Molekuler Senyawa Kuersetin dan Eugenol terhadap Protein Regulator Lintasan Penuaan SIR2, pada Khamir Saccharomyces cerevisiae Alfaridza, Annisa Nourma; Astuti, Rika Indri; Mubarik, Nisa Rachmania
Biota : Jurnal Ilmiah Ilmu-Ilmu Hayati Vol 10, No 1 (2025): February 2025
Publisher : Universitas Atma Jaya Yogyakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24002/biota.v10i1.6819

Proses penuaan dapat dipengaruhi oleh beberapa faktor, seperti peningkatan cekaman oksidatif dan inflamasi di mana senyawa antioksidan seperti kuersetin dan eugenol dapat mengatasi hal tersebut. Kuersetin dan eugenol merupakan senyawa antioksidan yang dapat ditemukan di alam. Kuersetin dan eugenol memiliki aktivitas antioksidan pada sel khamir maupun sel mamalia. Namun, mekanisme kedua senyawa ini dalam meregulasi penuaan di level molekuler belum tersedia. Oleh karena itu, penelitian ini dilakukan dengan tujuan untuk mengetahui interaksi senyawa kuersetin dan eugenol pada protein Sir2 pada Saccharomyces cerevisiae yang memiliki peran sebagai regulator sistem penuaan. Penelitian menggunakan studi penambatan molekular dengan senyawa kuersetin dan eugenol sebagai ligan uji, sedangkan reseptornya menggunakan Sir2 asal Saccharomyces cerevisiae dengan kode PDB, 2HJH. Hasil penelitian menunjukkan bahwa senyawa kuersetin dan eugenol dapat berikatan secara molekuler dengan protein Sir2. Parameter afinitas ikatan (ΔG) dilihat dengan nilai negatif yang tinggi. Senyawa kuersetin memiliki afinitas ikatan (ΔG) sebesar -8.5 kkal/mol, sedangkan pada senyawa eugenol memiliki afinitas ikatan (ΔG) sebesar -6.5 kkal/mol. Selain itu, adanya ikatan kimia dan residu asam amino menunjukkan bahwa senyawa ligan uji memiliki potensi untuk bersaing dengan ligan alami. Namun, penelitian lebih lanjut diperlukan untuk menentukan efek ligan uji terhadap lintasan penuaan, in vivo.

Extracellular Metabolites of Clove-Endophytic Bacteria, Niallia nealsonii DCL1, Exhibit Potential Cellular Antioxidant and Antiaging Activities Salsabilah, Nadiyah; Prastya, Muhammad Eka; Astuti, Rika Indri
Biology, Medicine, & Natural Product Chemistry Vol 14, No 2 (2025)
Publisher : Sunan Kalijaga State Islamic University & Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14421/biomedich.2025.142.747-755

The clove plant, Syzygium aromaticum L., is a highly valued spice in Indonesia, recognized for its extensive applications in food preservation and medicinal uses. In a prior study, six endophytic bacteria were successfully isolated from clove leaves. One of these isolates, designated as DCL1, is a Gram-positive bacterium identified as Niallia nealsonii. This study aimed to determine the antioxidant and antiaging properties of the extracellular metabolite of DCL1. Extracellular metabolites were extracted with ethyl acetate and evaluated for antioxidant activity via the DPPH assay. Total phenolic and flavonoid compounds were also quantified with further metabolilte profiling using Liquid Chromatography Tandem-Mass Spectrometry (LC-MS/MS) analysis. Further study of antiaging activity was assayed using yeast model Schizosacchromyces pombe. The extract from N. nealsonii DCL1 cultures harvested at 28 and 40 hours yielded 0.01% and 0.009%, respectively. Our findings indicate that the 40-hour extract contains higher levels of phenolics (93.54 mg gallic acid equivalents/g extract) and flavonoids (12.09 mg quercetin equivalents/g extract) compared to the 28-hour extract. Additionally, the 40-hour extract exhibited greater antioxidant activity than the 28-hour extract, as demonstrated by DPPH (IC50 222 µg/mL) and ABTS (IC50 511.43 µg/mL) assays. Moreover, the 40-hour extract significantly prolonged the viability of S. pombe, suggesting its potential as an anti-aging agent. LC-MS/MS analysis identified several potential bioactive compounds, including gallic acid and N-carbamoyl-2,3-dihydroxybenzamide, which may contribute to its bioactivity. Ultimately, our study indicates that DCL1 40-h extract showed antiaging potential, which is promising as source and formulation of biopharmaceutical or cosmeceutical products.

Eugenol Exhibits Antimutagenic Activity in Model Yeast Schizosaccharomyces pombe by Regulating DNA Damage Repair System: A Transcriptomic Analysis Muhammad Zulfiqri, Aldy; Astuti, Rika Indri; Prastya, Muhammad Eka
HAYATI Journal of Biosciences Vol. 32 No. 6 (2025): November 2025
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.32.6.1538-1550

Free radicals that accumulate in cells can cause oxidative imbalance and trigger oxidative stress at the cellular level. Such conditions lead to damage to genetic material that accelerates cellular aging. Plant secondary metabolites have been reported to exhibit antioxidant activities that have the potential to overcome oxidative stress. Eugenol, derived from cloves (Syzygium aromaticum), has been shown to possess antioxidant activity in vitro. However, there is no information on the antioxidative activity of eugenol at the cellular level. Our study focused on the effect of eugenol as an antigenotoxic agent in preventing DNA damage caused by oxidative stress treatment. Further analysis on the cellular levels of eugenol was done through a transcriptomics study in the model yeast Schizosaccharomyces pombe. Treatment with eugenol may increase the cell viability of yeast exposed to mutagenic UV and EMS, suggesting that eugenol can act as an antigenotoxic agent. Indeed, eugenol treatment can repair DNA damage as indicated by the DNA nicking assay. Eugenol showed potential as an antiaging agent by regulating the cell cycle of S. pombe, specifically by slowing down at the G1 phase and progressing towards the S phase. Transcriptomics analysis revealed that eugenol treatment can regulate genes related to DNA damage response, specifically mismatch repair, base excision repair, and Nucleotide excision repair, in the yeast S. pombe. Our data suggest that eugenol has the potential to regulate the oxidative stress-induced DNA damage response in yeast S. pombe, which supports cell longevity.

In silico characterization of adh1 gene encoding alcohol dehydrogenase 1 (ADH1) from non-conventional yeast, Wickerhamomyces and Pichia spp HARTONO, FAISAL DINIAMAL; MERYANDINI, ANJA; ASTUTI, RIKA INDRI
Jurnal Natural Volume 25 Number 3, October 2025
Publisher : Universitas Syiah Kuala

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24815/jn.v25i3.45843

Wickerhamomyces anomalus and Pichia kudriavzevii have high potential to produce bioethanol under high stress condition, due to their stress-tolerant properties. To elucidate and develop an efficient and sustainable bioethanol production, characterization of ethanol fermentation reactions is highly substantial. Ethanol fermentation employs key enzyme ADH1 encoded by ADH1 gene, important for conversion of acetaldehyde to ethanol. However, structural studies about alcohol dehydrogenase1 from these genera of yeasts are limited. This study aimed to detect the alcohol dehydrogenase 1 gene from Pichia spp. Using computational-bioinformatics approaches. The adh1 gene was amplified by PCR, visualized by electrophoresis, and analysed for sequence homology by BlastN and BlastP. The enzyme structure was constructed by SWISS-MODEL and I-TASSER with validation by Ramachandran plot, QMEAN4, and Local Quality Estimate. The Similarity and homology analysis of ADH1 genes and their corresponding protein sequence of yeast isolates showed that the ADH1gene was successfully detected. Multiple sequence alignment (MSA) and phylogenetic tree revealed that W. anomalus BT1-BT6 has close evolutionary relationship with ADH1 from Saccharomyces cerevisiae sequence while P. kudriavzevii IP4 showed different pattern. The ADH 1 enzyme model, generated using the SWISS-MODEL web server, demonstrated the best stereochemical quality, with a Ramachandran plot value of 100% for W. anomalus BT1 and 99.3% for P. kudriavzevii IP4. Superimposition of 3D-predicted model of ADH1 from W. anomalus BT1 and P. kudriavzevii 1P4 showed an exact match with amino acid in Zn2+ binding sites, confirming the ADH1 metaloenzyme properties. These findings provide structural insights about ADH1 genes and protein properties which can be used further for the development of efficient and high productivity of bioethanol productions through genetic and protein engineering.

IN SILICO ANALYSIS ON BINDING ACTION OF TERPENE NATURAL COMPOUNDS FROM APOCYNACEAE FAMILY AGAINST SHV-1 BETA-LACTAMASE FROM Klebsiella pneumoniae A M Sabbah, Sajida; Indri Astuti, Rika; Budiarti, Sri
BIOMA : Jurnal Ilmiah Biologi Vol. 14 No. 2 (2025): October 2025
Publisher : Prodi Pendidikan Biologi, FPMIPATI, Universitas PGRI Semarang

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.26877/585f2k97

Antibiotic resistance is a growing threat to public health, particularly with hospital-acquired infections caused by Klebsiella pneumoniae. The limited treatment options for these infections are further complicated by the emergence of antibiotic-resistant strains due to the overuse of antibiotics. This study investigates the potential of Monoterpene Indole Alkaloids (MIAs) derived from six genera within the Apocynaceae family as inhibitors of the beta-lactamase enzyme (bla-SHV-1), which plays a key role in antibiotic resistance in Klebsiella pneumoniae. Using the PyRx program for molecular docking, we assessed the binding affinity and interaction profiles of various MIAs with bla-SHV-1. Our results identified Paucidisine, (-)-19-Oxoisoeburnamine, and Paucidactine A as the most promising candidates, based on their interaction energies and binding modes. Detailed analysis of ligand-protein interactions, including hydrogen bonds and hydrophobic interactions, revealed that these MIAs exhibit higher binding affinity and structural similarity to the native ligand bla-SHV-1. While these findings are promising, it is important to note that they are based on in silico models. Further in vitro and in vivo studies are required to validate the efficacy and safety of these MIAs as potential therapeutic agents. This research marks a significant step towards developing alternative treatment options for antibiotic-resistant Klebsiella infections, potentially improving patient outcomes and addressing the global challenge of antibiotic resistance. In conclusion, our study offers novel insights into the potential use of MIAs as inhibitors of bla-SHV-1, contributing to the ongoing efforts to combat antibiotic resistance. Future research should focus on validating these in silico results through rigorous experimental and clinical studies, considering the ethical implications of introducing new treatments.

Interaksi Molekuler Senyawa Kuersetin dan Eugenol terhadap Protein Regulator Lintasan Penuaan SIR2, pada Khamir Saccharomyces cerevisiae Alfaridza, Annisa Nourma; Astuti, Rika Indri; Mubarik, Nisa Rachmania
Biota : Jurnal Ilmiah Ilmu-Ilmu Hayati Vol 10, No 1 (2025): February 2025
Publisher : Universitas Atma Jaya Yogyakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24002/biota.v10i1.6819

Proses penuaan dapat dipengaruhi oleh beberapa faktor, seperti peningkatan cekaman oksidatif dan inflamasi di mana senyawa antioksidan seperti kuersetin dan eugenol dapat mengatasi hal tersebut. Kuersetin dan eugenol merupakan senyawa antioksidan yang dapat ditemukan di alam. Kuersetin dan eugenol memiliki aktivitas antioksidan pada sel khamir maupun sel mamalia. Namun, mekanisme kedua senyawa ini dalam meregulasi penuaan di level molekuler belum tersedia. Oleh karena itu, penelitian ini dilakukan dengan tujuan untuk mengetahui interaksi senyawa kuersetin dan eugenol pada protein Sir2 pada Saccharomyces cerevisiae yang memiliki peran sebagai regulator sistem penuaan. Penelitian menggunakan studi penambatan molekular dengan senyawa kuersetin dan eugenol sebagai ligan uji, sedangkan reseptornya menggunakan Sir2 asal Saccharomyces cerevisiae dengan kode PDB, 2HJH. Hasil penelitian menunjukkan bahwa senyawa kuersetin dan eugenol dapat berikatan secara molekuler dengan protein Sir2. Parameter afinitas ikatan (ΔG) dilihat dengan nilai negatif yang tinggi. Senyawa kuersetin memiliki afinitas ikatan (ΔG) sebesar -8.5 kkal/mol, sedangkan pada senyawa eugenol memiliki afinitas ikatan (ΔG) sebesar -6.5 kkal/mol. Selain itu, adanya ikatan kimia dan residu asam amino menunjukkan bahwa senyawa ligan uji memiliki potensi untuk bersaing dengan ligan alami. Namun, penelitian lebih lanjut diperlukan untuk menentukan efek ligan uji terhadap lintasan penuaan, in vivo.

Enhanced Lipase Production in Pichia pastoris via Multiple Copies of Bacterial Lipase Genes and Co-expression of the HAC1 Gene Puspitasari, Esti; Rustam, Yepy Hardi; Satya, Andreas Adhi; Suwanto, Antonius; Wahyudi, Aris Tri; Astuti, Rika Indri
HAYATI Journal of Biosciences Vol. 33 No. 2 (2026): March 2026
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.33.2.288-296

The hac1 gene, a key regulator of the untranslated protein response (UPR), was co-expressed in Pichia pastoris GS115 to enhance the production of a lipase from Geobacillus stearothermophilus. Multicopy lipase constructs (1X and 4X) were transformed with pPICZAwbe_hac1, generating GS115/T1.2RQ(1X)_hac1 and GS115/T1.2RQ(4X)_hac1 strains. The GS115/T1.2RQ(1X)_hac1 strain showed an 186% lipase activity after 120 hours versus the control (100%), while the GS115/T1.2RQ(4X)_hac1 strain showed a faster initial increase (38% at 48 hours) and 28% at 120 hours, which was beneficial for efficient enzyme production. Overexpression of the hac1 gene enhances lipase production because it activates UPR genes when the endoplasmic reticulum is stressed due to a large number of recombinant proteins and forms proteins that are not appropriately folded. SDS-PAGE and tributyrin plate assays confirmed extracellular lipase expression (~43 kDa). These results demonstrate that hac1 co-expression significantly (p = 0.01) enhances lipase production in Pichia pastoris, especially in lower-copy constructs. This is the first report of co-expressing hac1 with Geobacillus stearothermophilus lipase genes in yeast. The findings are expected to contribute to developing more efficient microbial cell factories for producing industrial enzymes.

PENGEMBANGAN GALUR Pichia kudriavzevii TOLERAN CEKAMAN OSMOTIK GLUKOSA MELALUI EVOLUSI LABORATORIUM ADAPTIF Sidiq, Muhammad Raffel; Astuti, Rika Indri; Meryandini, Anja
Berita Biologi Vol 24 No 2 (2025): Berita Biologi
Publisher : BRIN Publishing (Penerbit BRIN)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.55981/berita_biologi.2025.9025

Bioetanol merupakan salah satu komoditas energi terbarukan terbesar di dunia di samping biodiesel. Efisiensi proses fermentasi etanol dapat dilakukan melalui penggunaan khamir fermentatif yang toleran cekaman fermentasi di antaranya cekaman osmotik yang dapat terjadi akibat penggunaan konsentrasi glukosa tinggi sebagai substrat fermentasi. Penelitian ini bertujuan untuk mengkonstruksi khamir mutan Pichia kudriavzevii galur RWT yang toleran cekaman osmotik glukosa melalui teknik evolusi laboratorium adaptif. Khamir P. kudriavzevii toleran cekaman omostik glukosa 35% berhasil diperoleh dan diberi kode isolat P. kudriavzevii RM. Namun, P. kudriavzevii RM tumbuh optimum pada kadar glukosa 20% dan tidak memiliki perbedaan morfologi dengan isolat tipe liarnya (RWT). Isolat khamir mutan memiliki fase log yang lebih lama dibandingkan isolat tipe liarnya (RWT) dan khamir etanologenik Saccharomyces cerevisiae. Hal ini mengindikasikan potensinya sebagai agen fermentasi bioetanol, karena bioetanol diproduksi pada fase pertumbuhan ini. Melalui pengamatan aktivitas mitokondria diketahui terjadi pergeseran sistem metabolisme dari respirasi aerobik menjadi fermentatif terlihat pada khamir P. kudriavzevii mutan ketika ditumbuhkan pada medium dengan kadar glukosa 20%. Penelitian lebih lanjut terkait produktivitas khamir mutan P. kudriavzevii mutan osmotoleran dalam memproduksi etanol perlu dilakukan untuk pemanfaatannya sebagai agen fermentasi.

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