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Search Results: 1 - 10 of 726 matches for " ARIS TRI WAHYUDI "
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Involvement of a Gene Encoding Putative Acetate Kinase in Magnetosome Synthesis in Magnetospirillum magneticum AMB-1
ARIS TRI WAHYUDI
HAYATI Journal of Biosciences , 2006,
Abstract: A nonmagnetic mutant of Magnetospirillum magneticum AMB-1, designated NMA40, was constructed by mini-Tn5 transposon mutagenesis to identify genes involved in magnetosome synthesis. Transposon delivery was carried out through conjugation between M. magneticum AMB-1 as a recipient and Escherichia coli S17-1 (λ pir) carrying pUTmini-Tn5Km1 as a donor strain. NAM40 did not respond to the magnetic fields and completely lacked of magnetosome in the cell. DNA sequence/gen interrupted by transposon (called flanking DNA) was isolated by inverse PCR and cloned into pGEM-T Easy. Alignment of the DNA sequence of the flanking DNA allowed the isolation of an open reading frame (ORF2) within an operon consisting of three genes. The amino acid sequence deduced from ORF2 showed homology with acetate kinase from Sinorhizobium meliloti (50% identity and 67% similarity), which function for acetate metabolism. Further analysis revealed that upstream of ORF2 is ORF1, had homology with phosphotransacetylase of S. meliloti (67% identity, 77% similarity), and ORF3 located downstream of ORF2, had homology with hypothetical protein of Thermotoga maritima (30% identity, 60% similarity). ORF2 was subsequently isolated, cloned, and overexpressed in Escherichia coli BL21 (DE3) pLysS as an ORF2-Histag fusion polypeptide.
Rapid and Simple Amplification of Genomic DNA Sequences Flanking Transposon
ARIS TRI WAHYUDI
Microbiology Indonesia , 2007,
Abstract: A rapid and simple method to amplify genomic DNA sequences flanking mini-Tn5 transposon insertion wasdeveloped. This technique can be used to determine the location and orientation of the transposon insertion within genomic DNA of the bacteria. Based on the mini-Tn5Km1 transposon sequence, PCR primers can be designed to specifically amplify the DNA sequences flanking mini-Tn5 transposon by inverse polymerase chain reaction (inverse PCR) directly, upstream and downstream of the transposon insertion. The method involves: (i) digestion with a restriction enzyme that does not cut mini-Tn5Km1 sequence; (ii) self-ligation under conditions favoring the production of monomeric circles; and (iii) inverse PCR reaction using primers designed from mini-Tn5Km1 sequence to amplify the DNA sequences flanking mini-Tn5Km1 transposon insertion. Feasibility and reliability of this method were demonstrated with mini-Tn5Km1 mutants of the microaerobic magnetic bacterium Magnetospirillum magneticum AMB-1 which are defective in magnetosomes synthesis. The inverse PCR products amplified from these mutant genomes showed the correct fragments as determined through Southern hybridization and DNA sequence analysis.
CLONING OF A GENE ENCODING PROTEIN BELONGING TO ABC TRANSPORTER INVOLVED IN BACTERIAL MAGNETIC PARTICLE SYNTHESIS IN MAGNETOSPIRILLUM MAGNETICUM AMB-1
ARIS TRI WAHYUDI
BIOTROPIA : the Southeast Asian Journal of Tropical Biology , 2009,
Abstract: Magnetospirillum magneticum AMB-1 synthesizes intracellular magnetic particles, magnetite (Fe3O4), enveloped by membrane called magnetosome under micro-aerobic conditions. Initial study of random transposon-based mutagenesis generated 62 nonmagnetic mutants of AMB-1 in a mini-Tn5 library. In order to identify a gene involved in bacterial magnetic particle (BMP) synthesis in the magnetic bacterium M. magneticum AMB-1, a nonmagnetic mutant from the library designated as NMA38-4, was analyzed. h e amino acid sequence deduced from the gene directly interrupted by transposon, ORF4 (1482 bp), showed homology to ATP binding cassette (ABC) transporter of Mesorhizobium loti with 62 % identity and 74 % similarity. It was strongly indicated by the occurrence of putative consensus sequence of ATP-binding motifs (ATP-binding protein). h e ORF4 was subsequently cloned in pET-15b and the recombinant ORF4-Histag fusion protein was heterologously expressed in Escherichia coli BL21 (DE3) pLysS. A 55 kDa protein corresponding to the ORF4-Histag fusion protein was obtained after purifi cation using Ni-NTA column. h is is the fi rst report describing a gene cluster containing gene encoding protein belonging to ABC transporter organized in an operon which is involved in BMP synthesis.
Screening and Characterization of Protease Inhibitors from Marine Bacteria Associated with Sponge Jaspis sp.
ARIS TRI WAHYUDI,QATRUNNADA,NISA RACHMANIA MUBARIK
HAYATI Journal of Biosciences , 2010,
Abstract: Three isolates among 138 sponge-associated bacteria were isolated from Waigeo Island, Raja Ampat West Papua Province, Indonesia, have been shown protease inhibitory activity against subtilisin (serine protease), thermolysin (metalloprotease), and crude extract from pathogenic bacteria (Eschericia coli enteropathogenic/EPEC K.1.1, Staphylococcus aureus, and Pseudomonas aeruginosa). Those three isolates were designated as sponge associated bacteria SAB S-12, SAB S-21, and SAB S-17. A simple casein and Sea Water Complete (SWC) double layer agar method was used to screen the bacteria against pathogenic bacteria producing protease, i.e. EPEC K.1.1, S. aureus, and P. aeruginosa. Among them, SAB S-12 isolate showed no inhibitory zone indicated. The isolate had the highest inhibitory activity against subtilisin and crude extract enzyme of pathogenic bacteria, the inhibitory activity was 91.6 and 98.9%, respectively. In addition, the SAB S-21 isolate had the highest inhibitory activity against thermolysin, it was 70.4%. The optimum pH and temperature for protease inhibition of the three isolates was at pH 7.0-8.0 and 40-50 oC respectively. Based on 16S rRNA gene sequence, the closest related with SAB S-12, SAB-17, and SAB-21 isolates was Providencia sp. (92% identity), Paracoccus sp. (86% identity), and Bacillus sp. (% identity), respectively.
Evidence for a Link Between Pathogenicity and the Role of ImpBacterial Transport Effector Proteins in Soybean Infection by Xanthomonas axonopodis pv. glycines
ANTONIUS SUWANTO,ARIS TRI WAHYUDI,BUDI TJAHJONO
Microbiology Indonesia , 2007,
Abstract: Xanthomonas axonopodis pv. glycines (Xag) is the causal agent of bacterial pustule disease of soybeans. A nonpathogenic mutant of Xag (M715) was constructed employing transposon mutagenesis which showed similar epiphytic survival in planta to its wild type strain (YR32). The objective of this work was to identify and to analyze genes involved in pathogenicity in Xag YR32. Inverse Polymerase Chain Reaction (IPCR) was used to isolate the DNA flanking transposon insertion. A 1.3 kb flanking DNA fragment was sequenced and analyzed employingBLAST program to study homology, the position of transposon insertion and to predict the structure and function of the gene. One of the Open Reading Frames (ORFs) shared homology with inner membrane proteins (imps) of Xanthomonas axonopodis pv. citri (GenBank accession No. NC 003919). Northern blot analysis revealed that an imps gene was monocistronic and the size of imps mRNA in YR32 was slightly longer than in M715. Reverse Transcriptase-PCR analysis demonstrated that the imps transcript in M715 was much less abundant than in the wild type YR32. Transposon (mini-Tn5-Kmr-Tpr) was determined to be inserted close to the end of C-terminal region of imps gene and might be sufficient to destabilize the imps transcript in M715 and so influence effectors transportation from Xag to plant cell.
Potential Pseudomonas Isolated from Soybean Rhizosphere as Biocontrol against Soilborne Phytopathogenic Fungi
ARI SUSILOWATI,ARIS TRI WAHYUDI,YULIN LESTARI,ANTONIUS SUWANTO
HAYATI Journal of Biosciences , 2011,
Abstract: Plants are liable to be attacked by soilborne fungal pathogens which are responsible to reduce plant growth and losses in yield. In Indonesia, indigenous soybeans’ rhizobacteria such as antifungal producing Pseudomonas sp. have not many been reported yet. Therefore, the potential of the Pseudomonas sp. as biocontrol agent should be deeply explored. The aim of this study was to screen the indigenous soybeans’ rhizobacteria Pseudomonas sp. that possessing biocontrol characters against soilborne mainly i.e. Sclerotium rolfsii, Fusarium oxysporum, and Rhizoctonia solani, in vitro and in planta. Eleven isolates identified Pseudomonas sp. CRB numbered by CRB-3, CRB-16, CRB-17, CRB-31, CRB-44, CRB-75, CRB-80, CRB-86, CRB-102, CRB-109, and CRB-112 were affirmed to be candidates of biocontrol agents toward the soilborne fungal pathogens. Pseudomonas sp. CRB inhibited growth of the pathogenic fungi approximately 11.1-60.0% in vitro. Among of them, 7 isolates were also produced siderophore, 2 isolates produced chitinase, and 4 isolates produced hydrogen cyanide. Seed coating with the Pseudomonas sp. CRB accomplished disease suppression in planta about 14.3-100% in sterile soil condition and 5.2-52.6% in non sterile soil condition. Consistency in high performance more than 30% of disease suppression in non sterile soil condition suggested that 5 isolates i.e. CRB-16, CRB-44, CRB-86, CRB-102, and CRB-109 isolates have great promising to be developed as biocontrol agents of soilborne pathogenic fungi.
Diversity of Antifungal Compounds-Producing Bacillus spp. Isolated from Rhizosphere of Soybean Plant Based on ARDRA and 16S rRNA
ARIS TRI WAHYUDI,BRAMANTYO JATI PRASOJO,NISA RACHMANIA MUBARIK
HAYATI Journal of Biosciences , 2010,
Abstract: Plant growth promoting rhizobacteria (PGPR) play an important role in improvement of seed germination, root development, and water utilization by plants. These rhizobacteria can stimulate plant growth directly by producing growth hormones or indirectly by producing antifungal compounds/antibiotics to suppress phytopathogenic fungi. The objective of this research was to analyze the diversity of 22 antifungal-producing rhizobacteria of Bacillus sp. isolated from rhizosphere of soybean plant based on Amplified rDNA Restriction Analysis (ARDRA) and 16S rRNA Sequence. Restriction enzymes in ARDRA analysis, HinfI, HaeIII, and RsaI were used to digest 22 16S rDNA amplified from Bacillus sp. genomes. Based on this analysis, genetic diversity of 22 Bacillus sp. producing antifungal compounds were classified into eight different groups. Moreover, six selected isolates randomly from each ARDRA group that have strong activity to suppress fungal growth were analyzed for their 16S rDNA sequences compared with reference strains. The distributions of these isolates were genetically diverse on several species of Bacillus sp. such as B. subtilis, B. cereus, and B. fusiformis. ARDRA is a reliable technique to analyze genetic diversity of Bacillus sp. community in the rhizosphere.
Xanthomonas oryzae pv oryzae the Causal Agent of Bacterial Leaf Blight of rice: Isolation, Characterization, and Study of Transposon Mutagenesis
Aris Tri Wahyudi,Siti Meliah,Abdjad Asih Nawangsih
Makara Seri Sains , 2011,
Abstract: Xanthomonas oryzae pv oryzae the Causal Agent of Bacterial Leaf Blight of rice: Isolation, Characterization, and Study of Transposon Mutagenesis. X. oryzae pv. oryzae (Xoo) causes bacterial leaf blight (BLB) of rice (Oryza sativa L.), a major disease that constrains production of the staple crop in many countries of the world. Identification of X. oryzae pv. oryzae (Xoo) was conducted based on the disease symptoms, pathogenicity, morphological, physiological, and genetic characteristics of bacterial cultures isolated from the infected plants. Fifty bacterial isolates predicted as Xoo have been successfully isolated. They are aerobic, rod shaped, and Gram negative bacteria. The isolates were evaluated for their hypersensitivity in tobacco and pathogenicity in rice plant. Fifty isolates induced hypersensitive reaction in tobacco and showed pathogenicity symptom in rice in different length. Based on physiological test, hypersensitivity and pathogenicity reactions, three bacterial isolates strongly predicted as Xoo, i.e. STG21, STG42, and STG46, were non indole formation, non pigment fluorescent, hydrolyzed casein, catalase activity positive, but negative oxidase. Partial sequencing of 16S rRNA genes of STG21 and STG42 showed 80% and 82% homology with X. oryzae, respectively, while STG46 showed 84% homology with X. campestris. Mini-Tn5 transposon mutagenesis of STG21 generated one of the mutants (M5) lossed it’s ability to induce hypersensitive reaction in tobacco plant and deficient in pathogenicity on rice. The lesion length of rice leaf caused by the mutant M5 decreased up to 80%.
Prospective Use of 1-Aminocyclopropane-1-Carboxylate Deaminase-Producing Bacteria for Plant Growth Promotion and Defense against Biotic and Abiotic Stresses in Peat-Soil-Agriculture
EDI HUSEN,ARIS TRI WAHYUDI,ANTONIUS SUWANTO,RASTI SARASWATI
Microbiology Indonesia , 2008,
Abstract: The 1-aminocyclopropane-1-carboxylate (ACC) deaminase (EC4.1.99.4) is an enzyme produced by some soil bacteria to degrade ACC (the immediate precursor of ethylene) to reduce ethylene biosynthesis in higher plants. Increased concentrations of ethylene in plant tissues, which are triggered by various biotic and abiotic stresses, inhibits plant growth and weakens the plant defense against the stressors. Various findings on the successful use of ACC deaminase producing bacteria for plant growth under unfavorable soil conditions are inspiring their use in tropical peat-soil-agriculture, which possesses bio-physical constraints. It has been proven that inoculation of plants with ACC deaminase producing bacteria decreased ethylene inhibition generated by unfavorable environmental conditions, such as nutrient shortage, flooding, drought, high salts, and the presence of heavy metals and organic pollutants. Understanding the mechanisms by which ACC deaminase-producing bacteria act to reduce plant stress and the fitness of bacterial traits with the properties and constraints of peat-soils becomes a key to utilize these bacteria in improving crop productivity. The bacteria may ameliorate plant stress as well as promote plant growth under seasonal bio-physical changes of peat-soils that are usually encountered in the field.
Genetic Diversity of Plant Growth Promoting Rhizobacteria of Bacillus sp. Based on 16S rRNA Sequence and Amplified rDNA Restriction Analysis
SYAMSUL BAHRI,ARIS TRI WAHYUDI,NISA RACHMANIA MUBARIK
Microbiology Indonesia , 2009,
Abstract: Plant-growth promoting rhizobacteria (PGPR) are rhizosphere associated soil-borne bacteria that can enhance plant growth and inhibit the development of root pathogens. Many soil bacteria have been used as PGPR, and one of them is Bacillus sp. The implementation of PGPR is constrained by genotype fluctuation that makes it inactive on the rhizosphere. Our previous study had characterized and revealed that 11 Bacillus sp. isolated from the soybean plant rhizosphere were PGPR. To asses and compare the genetic diversity of these isolates, Amplified Ribosomal DNA Restriction Analysis (ARDRA) and DNA sequence analysis of 16S rRNA were conducted. The construction of Neighbor-joining trees and bootstrap analysis of 100 resamples of ARDRA and 16S rRNA gene sequences were performed using Treecon software for windows ver. 1.3b. ARDRA analysis was done by using four restriction enzymes (RsaI, HaeIII, CfrI and HinfI), resulting in four phylotypes, respectively phylotype I (Bacillus sp. Cr24, Cr33, Cr64 and Cr68), phylotype II (Bacillus sp. Cr 31 and Cr66), phylotype III (Bacillus sp. Cr44 and Cr71) and phylotype IV (Bacillus sp. Cr67, Cr28 and Cr69). Results of BLASTN from 16S rRNA gene sequences showed that these isolates are genetically diversed. The evolution relationship of Bacillus sp. could be shown by the 16S rRNA gene sequences analysis, while ARDRA based on the digestion sites showed their variability.
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