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All Journal Vegetalika Indonesian Journal of Biotechnology ASEAN Journal on Science and Technology for Development
Muhammad Saifur Rohman
Departemen Mikrobiologi, Fakultas Pertanian, Universitas Gadjah Mada
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Computer Science & IT Immunology & microbiology Materials Science & Nanotechnology Mathematics

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Identification of Protease Producing Halophilic Bacteria from Bledug KuwuMud Volcano Muhammad Saifur Rohman; Irfan Dwidya Prijambada; Yohanna Anisa Indriyani; Heri Hendrosatriyo
Indonesian Journal of Biotechnology Vol 17, No 1 (2012)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (221.147 KB) | DOI: 10.22146/ijbiotech.15995

Abstract

The objective of this research was to isolate and identify the halophilic bacteria from Bledug Kuwu-mudvolacano having an ability to produce proteolytic enzyme. From this work, 6 bacterial isolates were obtainedfrom mud and water samples using artificial sea water media after incubation at room temperature. Threeout of the 6 isolates (BKL-3, BKL-5, and BKA-1) were selected for further analysis. BKL-3, BKL-5 and BKA-1exhibited an ability to grow at salt concentration greater than 10%. BKL-3 could grow on media supplementedwith 15% of salt, meanwhile BKL-5 and BKA-1 could grow at 20% of salt, respectively. Furthermore, thoseisolates also exhibited proteolytic activity when they were grown on casein media. The phylogenetic analysisbased on the 16SrRNA gene sequences showed that the BKL-3 belong to the group of Bacillaceae, whilst BKL-5and BKA-1 isolates were relatively distance from the group of Halomonadaceae. Therefore, BKL-5 and BKA-1could be considered as the allegedly new species that were separated from Halomonadaceae
The structural insight of class III of polyhydroxyalkanoate synthase from Bacillus sp. PSA10 as revealed by in silico analysis Listia Pradani; Muhammad Saifur Rohman; Sebastian Margino
Indonesian Journal of Biotechnology Vol 25, No 1 (2020)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.53717

Abstract

PhaC synthase is an enzyme responsible for PHA polymerization. In this work, the catalytic mechanism class III of PhaC synthase from Bacillus sp. PSA10 (BacPhaCSynt) was reported through in silico modelling approach based on the primary sequence of the PhaC synthase. The open reading frame BacPhaCSynt has been successfully isolated, cloned and overexpressed the recombinant protein in Escherichia coli BL21(DE3). To know the global architecture and catalytic mechanism, the structural prediction of BacPhaCSynt has been carried out by using MODELLER. The recombinant BacPhaCSynt exhibited monomeric molecular weight (MW) of 43.6 kDa, when it was analyzed on 12% SDS‐PAGE gel. Based on the structural prediction, BacPhaCSynt exhibited global architecture of α/β hydrolase fold, with the root mean square deviation (r.m.s.d) value of 0.94Å. The catalytic residues composition of BacPhaCSynt consists of C151, D307, and H336, but the H336 and D307 residues of the model have been distorted 62.8o and 175.2o from the corresponding residues of the template. Since the D307 is quite a distance from the H336, it might act as a general base for the activation of ‐OH group of the substrate. The results strongly suggested that the mode of action of BacPhaCSynt obeyed the covalent catalysis mechanism.
Pengaruh Kombinasi Pupuk Anorganik dan Vinase Diperkaya Mikrobia terhadap Pertumbuhan dan Hasil Jagung (Zea mays L.) Dyah Weny Respatie; Muhammad Saifur Rohman; Donny Widianto; Jaka Widada
Vegetalika Vol 9, No 4 (2020)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/veg.60497

Abstract

Penggunaan pupuk kimia dalam jangka panjang akan berdampak buruk bagi lahan pertanian, oleh karena itu diperlukan eksplorasi pupuk alternatif. Penelitian ini bertujuan untuk menentukan kombinasi pupuk NPK dan vinase diperkaya mikrobia yang memberikan pertumbuhan dan hasil jagung optimal serta mengetahui efektivitasnya dalam meningkatkan pertumbuhan dan hasil jagung. Penelitian dilaksanakan pada Februari - Juni 2020. Perlakuan disusun dalam rancangan acak kelompok lengkap (RAKL) faktor tunggal dengan tiga blok sebagai ulangan. Faktor yang diuji berupa kombinasi pupuk NPK standar (NPK majemuk + urea) dan vinase diperkaya mikrobia yang terdiri atas enam aras yaitu tanpa pupuk (P0), NPK standar yang terdiri dari 300 kg/ha NPK + 250 kg/ha urea (P1), vinase diperkaya mikrobia sesuai dosis anjuran 15000 L.ha-1 (P2), ¾ NPK standar + 15000 L.ha-1 vinase diperkaya mikrobia (P3), ½ NPK standar  + 15000 L.ha-1 (P4) dan ¼ NPK standar  + 15000 L.ha-1 vinase diperkaya mikrobia (P5). Data pengamatan dianalisis menggunakan ANOVA pada taraf  α = 5%  apabila terdapat beda nyata dilanjutkan dengan uji DMRT pada taraf  α = 5%. Kombinasi  3/4 NPK standar  + 15000 L.ha-1 (P3) memberikan pertumbuhan dan hasil jagung optimal yang sama baiknya dengan NPK standar (P1). Vinase diperkaya mikrobia sebanyak 15000 L.ha-1 yang dikombinasikan dengan ¾ NPK standar (P3) efektif meningkatkan pertumbuhan dan hasil jagung dengan nilai RAE >100%. Dari hasil tersebut menunjukkan bahwa vinase diperkaya mikrobia mampu mensubstitusi penggunaan pupuk kimia sebesar 25 % pada pertanaman jagung.
Manuka Honey Reduces the Virulence of Pectobacterium brasiliense by Suppressing Genes That Encode Plant Cell Wall-Degrading Enzymes Sheila Ava; Siti Subandiyah; Muhammad Saifur Rohman; Naoto Ogawa; Tri Joko
ASEAN Journal on Science and Technology for Development Vol. 39 No. 3 (2022): Land, Energy, and Water Resources
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29037/ajstd.880

Abstract

The primary virulence of soft rot pectobacteria, including Pectobacterium brasiliense, is mainly determined by the massive production of plant cell wall-degrading enzymes (PCWDEs), which promote plant tissue maceration in many crops. The antibiotic treatment to treat bacterial soft rot causes environmental problems and potentially affects resistance. Antibiotic resistance is driving interest in antimicrobial treatments, and no organism has been reported to have acquired resistance to honey. However, the use of honey as a therapeutic agent for plant bacterial pathogens has rarely been studied. Therefore, this study was undertaken to determine the in vitro effect of Manuka honey against P. brasiliense at the phenotypic and genotypic levels. A sublethal concentration of honey was determined by a growth inhibition assay in broth medium containing different concentrations of Manuka honey. A macerating assay was performed on orchid leaves, and the activities of the PCWDEs were examined in plate assays. The expression of PCWDE-associated genes was investigated using semi-quantitative reverse transcription-polymerase chain reaction analysis. The exposure of P. brasiliense to a sublethal concentration of Manuka honey significantly decreased the maceration ability of the orchid and the synthesis of PCWDEs, i.e., pectate lyase, polygalacturonase, and protease. Moreover, five PCWDEs-encoding genes, such as pelA, pelB, pelC, pehA, and prtW, had lower expression levels after the honey treatment compared with recA as the internal standard. The honey treatment decreased the virulence of P. brasiliense associated with the synthesis of PCWDEs. Therefore, Manuka honey reduced virulence by suppressing the expression of the PCWDE genes.
Co-Authors Donny Widianto Dyah Weny Respatie Heri Hendrosatriyo Irfan Dwidya Prijambada JAKA WIDADA Listia Pradani Naoto Ogawa Sebastian Margino Sheila Ava Siti Subandiyah Tri Joko Yohanna Anisa Indriyani