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Indrasumunar A.,University of Queensland | Indrasumunar A.,Indonesian Center for Agricultural Biotechnology | Gresshoff P.M.,University of Queensland
Plant Signaling and Behavior | Year: 2010

In symbiosis with Bradyrhizobium japonicum, soybean (Glycine max L.) forms nitrogen-fixing nodules in its roots after mitogenic stimulation from a bacterial lipo-oligosaccharide (the 'Nodfactor'). In our recent paper in Plant and Cell Physiology we utilize two recessive loss-of-function plant mutants with a non-nodulation phenotype, and comparative genomics to clone and functionally analyze relevant soybean genes of the LysM receptor kinase family which are needed for perception of Nod-factor released by its microsymbiont B. japonicum. Two highly related lipo-oligochitin LysM type receptor kinase genes were cloned; they are presumed to be the critical nodulation inducing (Nod) factor receptor. These duplicated receptor genes were called GmNFR5α and GmNFR5β. Non-sense mutations in GmNFR5α and GmNFR5β were functionally complemented by both wild-type GmNFR5α and GmNFR5β in transgenic roots, indicating that both genes are functional. Both genes are wild-type in some soybean cultivars; however, non-functional NFR5β alleles were discovered in several others, which harbored an identical 1,407 bp retroelement-type insertion. GmNFR5α but not GmNFR5β was expressed in tap and lateral root portions at about 10-25% of GmATS1 (ATP synthase subunit 1), but not in trifoliate leaves and shoot tips. In general, inoculation treatment downregulated GmNFR5α/β transcripts in tap and lateral root portions. © 2010 Landes Bioscience. Source

Mustopa A.Z.,Indonesian Institute of Sciences | Kusdianawati,University of Indonesia | Fatimah,Indonesian Center for Agricultural Biotechnology | Umami R.N.,Indonesian Institute of Sciences | And 2 more authors.
International Food Research Journal | Year: 2016

Heterologous protein expression has been used in attemp to increase bacteriocins yields by less laborius process. In this study, the plnEF genes (530 bp) encoding plantaricin S34 have been identified and cloned to pGEMTeasy s vector. Plantaricin S34 gene had 99% similarity with all those plnEF locus of Lactobacillus references strain aligned. Furthermore, plnE peptide of plantaricin S34 had unique one amino acid substitution at position 33 (lysine > cysteine), while two amino acids were substituted at position 14 (alanine > serine) and 42 (valine > isoleucine) appeared on plnF peptide. PCR amplification of mature fragment of plnE and plnF gene produced the bands with length of approximatly 102 bp and 105 bp respectively. Moreover, Both of fused recombinant plnE and plnF peptide have been expressed heterologously in E. coli as protein fusion with thioredoxin-(His)6tag with given molecular mass of approximatly 21 kDa for each peptides. Overall, the partial operon of plnEFI loci of L. plantarum S34 has been characterizied and the plnEF genes that composed this operon was successfully cloned and produced as hetelogous recombinant peptides. © 2008 IFRJ. Source

Indrasumunar A.,Indonesian Center for Agricultural Biotechnology | Indrasumunar A.,University of Queensland | Menzies N.W.,University of Queensland | Dart P.J.,University of Queensland
Soil Biology and Biochemistry | Year: 2012

A glasshouse experiment studied the role of calcium and pH on competitiveness of acid-sensitive and acid-tolerant Bradyrhizobium japonicum strains with similar N 2-fixation effectiveness in nodulating two soybean (Glycine max L. Merr) cultivars selected for tolerance of aluminium (PI416937) or for manganese (Manta). Liming provides calcium (Ca) as well as increasing soil pH. Thus the effect of Ca and pH of soil are difficult to separate. We examined the effects of Ca per se by comparing the response to gypsum and lime amendment on the competitiveness of acid-tolerant and acid-sensitive strains in nodulating soybean in an acid soil. Acid soil was treated with either CaSO 4 or CaCO 3 and incubated for 2 weeks before sowing soybean seed. Two acid-sensitive and two acid-tolerant B.japonicum strains were mixed with each other (one acid-sensitive plus one acid-tolerant) and were inoculated onto soybean seeds at the rate of 10 6cfuseed -1. Soil pH, as amended by lime addition, had more effect on nodulation than Ca addition in the form of gypsum. The response was affected by cultivar and strain in a complicated fashion with a marked strain×cultivar interaction. One acid-tolerant strain formed most nodules with both cultivars in the unamended soil of pH 4.36 in competition with one acid-sensitive strain. The same acid-tolerant strain was not competitive against the second acid-sensitive strain with Manta but was with PI416937. The second acid-tolerant strain was not competitive with either acid-sensitive strain in unamended and gypsum treated soils. It was only competitive with PI416937 in limed soil, a rather surprising result. Inoculation of this soil with no native soybean nodulating strains, increased shoot weight, %N, N uptake. N 2-fixation was greatly increased by inoculation and lime addition, and to a lesser extent by gypsum addition for Manta. This experiment indicates that addition of Ca per se as gypsum to an acid soil has little effect on symbiotic performance, but changing pH by liming has a major effect, that both soybean cultivar and B.japonicum strain influence the competitiveness of strains in acid soil and that acid-tolerance does not necessarily increase a strain's competitiveness. © 2011 Elsevier Ltd. Source

Waki T.,Tochigi Prefectural Agricultural Experiment Station | Horita M.,Japan National Institute for Agro - Environmental Sciences | Kurose D.,Japan National Institute for Agro - Environmental Sciences | Mulya K.,Indonesian Center for Agricultural Biotechnology | Tsuchiya K.,Kyushu University
Japan Agricultural Research Quarterly | Year: 2013

Asia-Pacific region was assessed by examining their biochemical properties, discriminating the phylogeny by polymerase chain reaction (PCR), and analyzing the egl and mutS gene sequences. These data were compared with those of reference strains covering the known diversity within the R. solanacearum species complex. Fifty-two of the Zingiberaceae plant isolates belong to either biovar 3 or biovar 4. Multiplex PCR analyses indicated that these strains belong to phylotype I. Phylogenetic analyses revealed that the investigated strains could be further divided into five or more groups and three major groups, based on the egl and mutS gene sequences, respectively. These groups were closely correlated with the host species and/or geographical origin. Our findings suggest that R. solanacearum strains affecting Zingiberaceae plants have multiple origins from within the Asia-Pacific region, and may have been disseminated with seed rhizomes. Source

Safitri H.,Indonesian Center for Rice Research | Purwoko B.S.,Bogor Agricultural University | Dewi I.S.,Indonesian Center for Agricultural Biotechnology | Ardie S.W.,Bogor Agricultural University
Journal of the International Society for Southeast Asian Agricultural Sciences | Year: 2016

Salt accumulation in irrigated soil is one of the main factors limiting rice productivity. A greenhouse experiment was conducted at Cimanggu Experiment Station, Bogor, Indonesia from May to September 2014 using a completely randomized design in a factorial arrangement with three replications. Four salt tolerant and two salt sensitive genotypes of rice were used in this experiment. The treatments were five concentrations of NaCl (0, 20, 40, 60 and 80 mM) applied on 21 day-old seedlings and maintained until harvest time. The study sought to evaluate the response of several rice genotypes to various NaCl concentrations through observation of morphological and physiological characters. The study showed that the increase of NaCl concentrations in soil significantly reduced plant height, number of panicles plant-1, panicle length, leaf length, 1000 grain weight, and grain yield. On physiological characters, salinity increased [Na+], decreased [K+] and [Ca2+] concentrations, and reduced K+/Na+ and Ca2+/Na+ ratios in the leaf tissue. The addition of 40 mM NaCl can distinguish tolerant and sensitive genotypes. The grain yield of sensitive genotypes decreased 90-100% at 40 mM NaCl, while the tolerant genotypes showed <70% in grain yield reduction. © 2016, International Society for Southeast Asian Agricultural Sciences. All Rights Reserved. Source

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