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Pemodelan protein dan analisis molecular docking enzim β-glukanase solat Bacillus subtilis W3.15: Ainia Hanifitri; Laksmi Ambarsari; Nisa Rachmania Mubarik
Menara Perkebunan Vol. 91 No. 1 (2023): 91 (1), 2023
Publisher : INDONESIAN OIL PALM RESEARCH INSTITUTE

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22302/iribb.jur.mp.v91i1.523

Abstract

The β-glucanase enzyme is an enzyme protein that can hydrolyze β-glucan, one of the main components of the fungal cell wall. This enzyme protein is produced by several bacteria, one of which is B. subtilis. The three-dimensional (3D) structure of proteins is necessary to understand their properties and functions of proteins. Enzyme proteins can be analyzed for their structure and function using in silico method. This study aims to detect the β-glucanase gene from B. subtilis W3.15 and analyze it using the in silico method. The methods in this research are homology modeling and molecular docking analyses. Modeling was carried out using the SWISS-MODEL server and docking analysis using the PLANTS 1.1 program. Modeling the β-glucanase enzyme is based on the template of the β-glucanase enzyme protein model with PDB code 3o5s. The results of sequence alignment and model visualization were quite good as indicated by the model having a Ramachandran Plot value in the favored area of 91.10 %, a MolProbity score of 0.95, and a QMEAN value of 0.90 ± 0.06. The β-glucanase enzyme model was then docked using the PLANTS1.1 program with native ligand B3P, 1,4-β-D-Glucan, D-glucose, β-D-Glucan from oats, and N-Acetyl glucosamine. The results of docking analysis showed that the β-glucan ligand (β-D-glucan from oats) used as a substrate in the cultivation of isolate B. subtilis W3.15 had a better binding energy prediction value compared to the B3P ligand, which is a natural ligand in the template proteins.   [Keywords: β-Glucan, β-D-Glucan from oat, ligand, PLANTS 1.1, 3D structure, SWISS-MODEL]
ISOLASI DAN KARAKTERISASI BAKTERI PENAMBAT NITROGEN INDIGENOUS POTENSIAL SEBAGAI PUPUK HAYATI DALAM REMEDIASI LAHAN BEKAS TAMBANG BATU KAPUR Mashudi, Mashudi; Mubarik, Nisa Rachmania
Purifikasi Vol 22 No 1 (2023): Jurnal Purifikasi
Publisher : Department of Environmental Engineering-Faculty of Civil, Planning, and Geo Engineering. Institut Teknologi Sepuluh Nopember, Surabaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.12962/j25983806.v22.i1.452

Abstract

Lahan bekas pertambangan umumnya memiliki struktur fisik dan kimia yang kurang optimum untuk pertumbuhan tanaman. Bakteri tanah indigenous dapat digunakan untuk membantu proses remediasi lahan bekas pertambangan dengan cara dimanfaaatkan sebagai pupuk hayati. Bakteri penambat nitrogen merupakan salah satu bakteri yang dapat membantu mempercepat remediasi tanah karena memiliki kemampuan memperkaya kandungan nitrogen dalam tanah. Penelitian ini bertujuan untuk mengisolasi dan melakukan karakterisasi bakteri penambat nitrogen dari tanah bekas tambang batu kapur di wilayah Cirebon, Jawa Barat. Isolasi bakteri dilakukan terhadap 13 sampel yang berasal dari area sekitar lahan bekas tambang batu kapur. Hasil isolasi diperoleh 6 isolat bakteri penambat nitrogen hidup bebas dan 2 isolat bakteri penambat nitrogen simbiosis. Seluruh isolat memiliki kemampuan menghasilkan Indole-3-acetic acid (IAA) jika ditambahkan 1 mM L-triptofan. Dua isolat dipilih (7B21Y dan 5A22) berdasarkan ciri morfologi sel dan koloni untuk dilakukan pengujian fisiologis. Aktivitas nitrogenase isolat 7B21Y dan 5A22 diukur dengan menggunakan Pengujian Reduksi Asetilen dan diperoleh masing-masing 7.09 ppm dan 5.59 ppm. Isolat 7B21Y kemudian diidentifikasi secara fisiologi menggunakan kit API dan diketahui memiliki kemiripan 99.9% dengan Rhizobium radiobacter.
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

Abstract

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.
Respon Pertumbunan Tanaman Kedelai terhadap Bradyrhizobium japonicum Toleran Masam dan Pemberian Pupuk di Tanah Masam Triadiati, ,; Mubarik, Nisa Rachmania; Ramasita, Yoan
Jurnal Agronomi Indonesia (Indonesian Journal of Agronomy) Vol. 41 No. 1 (2013): Jurnal Agronomi Indonesia
Publisher : Indonesia Society of Agronomy (PERAGI) and Department of Agronomy and Horticulture, Faculty of Agriculture, IPB University, Bogor, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (318.229 KB) | DOI: 10.24831/jai.v41i1.7072

Abstract

The use of acid tolerant rhizobacteria such as Bradyrhizobium japonicum is one effort for increasing soybeanproductivity in acid soil. B. japonicum is a N-fixing bacteria that can promote soybean growth through symbiosis with thehost plants. The objective of this study was to investigate the growth and production of soybean var. Wilis inoculated by B.japonicum and NPK inorganic fertilizer application in acid soil. Two isolates of B. japonicum that were BJ 11(19) and BJ11(wt) were used as inoculant for soybean. BJ 11(19) was resulted by transposons mutagenesis, whereas BJ 11(wt) is a wild type of bacteria. Both isolates of B. japonicum were acid tolerant. Soybean was inoculated with BJ 11(19) and BJ 11(wt)combined with compost and nitrogen fertilizer (with two rates). The field experiment was conducted at Cikabayan, Darmaga,in a randomized complete block design with 12 treatments and 3 replicates. The results showed that application of the acidtolerant B. japonicum BJ 11(wt), compost, and nitrogen fertilizer (10 g m-2) increased the plant height, dry weight of shootsand roots, nodule number, dry weight of nodules, nitrogenase activity, number of pod and seed, seed weight, and nitrogencontent of seeds in acid soil.Keywords: acid soil, acid tolerant rhizobia, Bradyrhizobium japonicum, compost, nitrogen fertilizer
Peningkatan akumulasi tiamin pada kultur Escherichia coli melalui peningkatan oksigenasi dan penghilangan rpoS Nuraliah Rusman; Prayoga Suryadarma; Nisa Rachmania Mubarik
AGROINTEK Vol 19, No 1 (2025)
Publisher : Agroindustrial Technology, University of Trunojoyo Madura

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21107/agrointek.v19i1.11110

Abstract

Microorganisms as cell factories in producing a product are strongly influenced by their metabolism. engineering microbial metabolism by increasing coenzymes that play a role in enzyme activity. Thiamine diphosphate is one of the coenzymes that are commonly found in the metabolic pathways of microbial cells. Increasing the thiamine formation pathway as a precursor in the thiamine metabolic pathway is a strategy in this study. Enhancing thiamine accumulation in Escherichia coli culture by inducing oxygenation level and deleting rpoS was investigated. The investigation was conducted by comparing the cultivation of  Escherichia coli BW25113 (parent strain) and BW25113-∆rpoS (rpoS mutant) cultures under aerobic conditions at different shaking rotation rates of 150 and 200 rpm. The measured parameters were thiamine accumulation, dry cell weight, acetate concentration and glucose consumption of the cultures. Inducing oxygenation level of parent strain cultures through increasing shaking rotation rate from 150 to 200 rpm induced 40 % thiamine accumulation. Meanwhile, deletion of rpoS increased 9,5 % thiamine accumulation compared to parent strain culture
Biocontrol Potential of Chitinase-Producing Soil Bacteria Against Fusarium proliferatum Wulandari Antika Putri; Nisa Rachmania Mubarik; Aris Tri Wahyudi
HAYATI Journal of Biosciences Vol. 33 No. 4 (2026): July 2026
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.33.4.1136-1146

Abstract

Fusarium proliferatum, a phytopathogenic fungus, causes significant agricultural losses. Chitinase-producing bacteria from post-mining soil have potential as biocontrol agents because they degrade chitin, a major component of fungal cell walls. This study aimed to isolate, characterize, and purify bacterial chitinase and evaluate its antifungal activity against F. proliferatum. Bacterial isolates were obtained from post-mining soil in Martabe and screened for chitinase activity using chitin agar medium. The selected isolates were identified through 16S rRNA gene sequencing, and the chitinase enzyme was partially purified using ammonium sulfate precipitation. The antifungal activity against F. proliferatum was evaluated using dual-culture and food-poisoning assays. Two isolates, TSU4 and TSU5, exhibited high chitinolytic activity with hydrolytic zone indices of 2.1±0.2 cm and 1.9±0.41 cm, respectively; TSU4 (Bacillus cereus) was selected for further study. The 70% ammonium sulfate-precipitated chitinase showed a specific activity of 15.66 U/mg, and the concentrated enzyme inhibited F. proliferatum growth by 33.8±0.23%. Chitinases belong to the glycoside hydrolase family 18 (GH18), an evolutionarily widespread group of chitin-degrading enzymes with a conserved catalytic domain that hydrolyzes β-1,4 linkages in chitin, making GH18 chitinases effective for degrading fungal cell walls in biocontrol applications. These findings indicate that the chitinase produced by B. cereus TSU4 shows significant antifungal activity and has strong potential as a biocontrol agent against F. proliferatum.
Isolation, Characterization, and Identification of Biosurfactant-Producing Bacteria from Palm Oil Mill Effluent Jezila Amana Nousra Atsemani; Nisa Rachmania Mubarik; Yuliana Maria Diah Ratnadewi
Jurnal Ilmu Pertanian Indonesia Vol. 31 No. 3 (2026): Jurnal Ilmu Pertanian Indonesia
Publisher : Institut Pertanian Bogor

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.18343/jipi.31.3.426

Abstract

Biosurfactants-producing bacteria are bacteria with the ability to produce natural surfactants that can degrade oil both in soil and water. Most of these biosurfactant-producing bacteria are often found in area polluted by grease or oil like palm oil mill effluent. The purpose of this research was to isolate, characterize, and identify biosurfactant-producing bacteria from palm oil mill effluent. This research was conducted using descriptive and identification methods through a general screening using oil displacement, drop collapse, and hemolysis assay, morphological characterization, emulsification tests and molecular identification for the bacteria with the highest emulsification index. Bacteria were isolated from palm oil wastewater by dilution method. In this study, 17 isolates were obtained with 2 isolates having the highest oil spreading results (SLP2.2 and SLP1.5). Both isolates showed negative hemolysis activity and were both identified as Gram-positive bacilli. Both isolates were cultivated for biosurfactant production and subsequent extraction. Crude biosurfactant extract was successfully obtained from isolate SLP2.2 with a yield of approximately 0.08 g/L. Emulsification index value of SLP2.2 extract was 36.93 ± 0.57%. SLP2.2 was identified as Cytobacillus kochii. This research provides microbial resources for microbial enhanced oil recovery and lays a foundation for practical application, such as sustainable bio-based products development.
Characteristics of Cellulase Producing Bacteria Isolated from Gold Mine Soil Fatmila Amirah Radwa; Nisa Rachmania Mubarik; Popi Asri Kurniatin
Jurnal Ilmu Pertanian Indonesia Vol. 31 No. 3 (2026): Jurnal Ilmu Pertanian Indonesia
Publisher : Institut Pertanian Bogor

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.18343/jipi.31.3.418

Abstract

Land degradation has created an urgent need for innovative restoration strategies based on microbial applications. The microbiological approach using cellulase enzymes produced by cellulolytic bacteria is a prospective step to address problems related to land restoration and biodegradation of complex organic matter in the environment. This study aimed to isolate and characterize cellulolytic bacteria from post-mining soil collected at the Martabe gold mine site in South Sumatra, Indonesia. Isolation and selection of cellulolytic bacteria was performed on 1% carboxymethyl cellulose (CMC) medium, resulting of two non-pathogenic Gram-positive isolates, TSUS3.4.1 and TSUS3.4.2, with cellulolytic index of 2.51 and 2.26, respectively. Hemolysis tests on blood agar confirmed the semi- and non-pathogenic activity of both isolates. The growth curve and enzyme-specific activity was tested and measured in minimal nutrition broth with addition of 1% CMC with the highest activity values of 0.37 U/mg for TSUS3.4.1 and 0.17 U/mg for TSUS3.4.2 at the 27th hour after incubation. TSUS3.4.1 isolate has optimum cellulase activity at pH 6 and 30°C. TSUS3.4.2 isolate has optimum cellulase activity at pH 7 and temperature 30°C. These findings highlight the isolates potential positioning them as promising candidates for biotechnological applications in post-mining land rehabilitation and organic waste degradation. Keywords: biodegradation, cellulolytic bacteria, cellulose, organic matters, post-mining
Selection and Identification of Potential Hydrolytic Bacillus from Litter Composting Ika Setianingsih; Nisa Rachmania Mubarik; Iman Rusmana
Jurnal Ilmu Pertanian Indonesia Vol. 31 No. 1 (2026): Jurnal Ilmu Pertanian Indonesia
Publisher : Institut Pertanian Bogor

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.18343/jipi.31.1.107

Abstract

Microbe study on degraded trash has been widely conducted, with the intention of improving the efficiency and effectiveness of waste processing. The purpose of this study was to select and identify hydrolytic Bacillus from litter composting. The samples were the litter composting outcomes with five different treatments, namely the inclusion of nutrient broth (NB), commercial formula, molasses, tryptic soy broth (TSB), and talcum, with each formula containing a microbial consortium. Bacteria were isolated using the serial dilution method. Each isolate was evaluated for its capacity to lyse red blood cells on blood agar media. Cellulolytic, amylolytic, and proteolytic bacteria were grown on nutritional agar media containing carboxy-methyl cellulose (CMC), starch, and skim milk. The antagonistic test involved testing isolates that hydrolyze all three types of substrates. Isolates that were not antagonistic to one another were identified based on phenotypes (colony and cell morphology using Gram staining) and genotypes (16S rRNA gene). Fourteen isolates of Bacillus sp. had cellulolytic, amylolytic, and proteolytic properties. Four isolates were chosen; two of them were comparable to Bacillus stercoris, while the other two, 5.5 and 5.9R, are similar to Calidifontibacillus erzurumensis and Bacillus amyloliquefaciens. Therefore, litter can be used to determine the hydrolytic capability of Bacillus isolates. Keywords: amylolytic, Bacillus, cellulolytic, proteolytic
Microorganism Formulation in Talcum and Molasses for the Organic Waste Biodrying Process Sukarya Zaenal Arifin; Nisa Rachmania Mubarik; Iman Rusmana
Jurnal Ilmu Pertanian Indonesia Vol. 31 No. 2 (2026): Jurnal Ilmu Pertanian Indonesia
Publisher : Institut Pertanian Bogor

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.18343/jipi.31.2.211

Abstract

The growing amount of waste needs the employment of ecologically friendly technologies to reduce the likelihood of environmental hazards. Biodrying is a bioenergy processing technique that uses waste to minimize water content while increasing calorific value and temperature, indicating its potential as a renewable energy source. The purpose of this study was to apply a microbial consortia formulation containing talc and molasses to the biodrying process of organic waste, to assess the effect of carrier materials on biodrying performance, and to identify the ideal period for the process. The microbial consortium used included Bacillus thuringiensis SAHA 12.12, Lactiplantibacillus plantarum IN05, Rhizobium sp. RIKG, Saccharomyces cerevisiae L1, Streptomyces sp. A4J, and Trichoderma sp. T2J, all of which were from the IPB Microbiology Laboratory collection. The use of a microbial consortium showed an impact on the measurable results of biodrying organic waste, such as calorific value, water content, and weight reduction. Molasses formulation can boost biodrying efficiency (0.57), calorific value (118−129%), water content (56%), weight loss (34.5%), C/N ratio (32%), and higher temperatures when compared to other carrier materials. Inclusion of talc gives a longer shelf life than molasses. As a result, a molasses-based formulation has the potential to improve biodrying efficiency, while talc can extend the shelf life of the microbial community. Keywords: biodrying, microbial consortium, molasses, organic waste, talc.
Co-Authors . QATRUNNADA Aas Ratnasari Ahmad Suryadi Ainia Hanifitri AINISSYA FITRI Alfan Cahyadi Alfaridza, Annisa Nourma ALINA AKHDIYA Andreas Adhi Satya Andreas Adhi Satya ANGELIA REZTY FITRIANI SITUMORANG Anggreandari, Rizky Ani Suryani Ani Suryani Anja Meryandini Antonius Suwanto Anuraga Jayanegara ARIO BETHA JUANSSILFERO Aris Tjahjoleksono Aris Tri Wahyudi Atang Sutandi Ayni, Qurrotu Bambang - Riyanto Besty Maranatha BRAMANTYO JATI PRASOJO Budiasih Wahyuntari Budiasih Wahyuntari Budiasih Wahyuntari Cahyadi, Alfan CUCU WIJAYANTI Dadang Suhendar Dadang Suhendar DEBI ARIVO Delfi Trisnawati DERI YURATMOKO Desniar - - Dewi Seswita Zilda Dewi Seswita Zilda Dewinta Nur Alvionita Diah Ratnadewi Dian Syahfitri Dinamella Wahjuningrum Dudi Firmansyah Dwi Ambarawati Dwi Andreas Santosa Ekowati Chasanah Encah Ewi Mulyeti Esti Puspitasari ESTI PUSPITASARI Evi Damayanti Evi Damayanti, Evi Fahmi, Riziq Ilham Nur Fatmila Amirah Radwa Fauzy Rachman Fauzy Rachman Fauzy Rachman Ferymon Mahulette Ferymon Mahulette Ferymon Mahulette, Ferymon Fitratul Aini Fitratul Aini, Fitratul Fitriani Idham Galih Cendana Nabilasani Galih Cendana Nabilasani GENIA SOTYA SINARAWADI Hadi Susilo Hamim Hamim Hana Nurullita Prestisia Hasrul Satria Hasrul Satria, Hasrul HENDRA PARDEDE Hirmas Fuady Putra Idin Abidin Ika Roostika Tambunan, Ika Roostika Ika Setianingsih Iman Rusmana Irmanida Batubara Ismi Isti'anah Isna Rahma Dini Iswati, Ruma It Jamilah Ivan Permana Putra Jepri Agung Priyanto Jepri Agung Priyanto, Jepri Agung Jezila Amana Nousra Atsemani Karina Eku Dwinanda Gunawan KI AGENG SARWONO Kusuma Handayani LAKSMI AMBARSARI Latusi Anggriani Lia Siti Nur'amaliyah Lia Siti Nur'amaliyah LISDAR A. MANAF Lisdar Idwan Sudirman Listyowati, Sri lmiah, Sitti Nur Luky Adrianto Maggy Thenawidjaya Suhartono Maherani, Vincentia Fenice Angger Maranatha, Besty Maria Dita Febriani Lumban Gaol Marini Adani Mashudi Mashudi Masrukhin Masrukhin MIFTAHUL KHAIRAH Muhamad Azwar Syah MUHAMMAD EKA PRASTYA Muhammad Ridla Mulyorini Rahayuningsih Mutiha Panjaitan Nabilasani, Galih Cendana Nabilasani, Galih Cendana Ninda Ningtyas Nuraliah Rusman Nurul Hidayati ORHINTA MUTIARA JATI Partomuan Simanjuntak Partomuan Simanjuntak Partomuan Simanjuntak Popi Asri Kurniatin Prayoga SURYADARMA Puspita Lisdiyanti Rika Indri Astuti RIMA ERNIA Risky Hadi Wibowo Risky Hadi wibowo Rizky Anggreandari ROHMATUSSOLIHAT ROHMATUSSOLIHAT RONI RIDWAN Rury Eryna Putri Rury Eryna Putri RUSLI FIDRIYANTO Sarah Asih Faulina Sarah Asih Faulina, Sarah Asih Sipriyadi Sipriyadi Sipriyadi Siswa Setyahadi Siswodarsono, Trismilah Siswodarsono, Trismilah Siti Azzira Rahma Sitti Nur Ilmiah Sonya Tobing SRI BUDIARTI Sri Budiarti Poerwanto Sri Listyowati SRI RAHAYU Suhendar, Dadang Suhendar, Dadang Sukarya Zaenal Arifin SYAMSUL BAHRI SYAMSUL BAHRI TEDJA IMAS Thenawidjaya, Maggy Titi Candra Sunarti TRI ASMIRA DAMAYANTI Tri Handayani Kurniati Tri Handayani Kurniati Triadiati Triadiati Trismilah Trismilah Siswodarsono Untung Sudadi Wahyu Widosari Wibowo, Risky Hadi WIDANARNI WIDANARNI Widosari, Wahyu Wulandari Antika Putri WULANSIH DWI ASTUTI YANTYATI WIDYASTUTI Yoan Ramasita Yusro Nuri Fawzya Zaenal Arifin, Sukarya ZETRYANA PUTERI TACHRIM Zulfarina Zulfarina Zulfarina,