Authors:I. Tóbiás, N. Bakardjieva, and L. Palkovics
Maize dwarf mosaic is the most widespread virus disease affecting corn production in Hungary and Bulgaria. Samples from virus infected maize were collected from different part of Bulgaria and employed test plants, ELISA serological method and RT-PCR in order to identify the viral pathogen.
Maize dwarf mosaic virus
(MDMV) was detected in all tested samples. For further investigation three MDMV isolates were selected and cloned. Cloned cDNAs representing the coat protein gene of the virus have been sequenced. The coat protein genes of Bulgarian and Hungarian isolates of MDMV were compared. The nucleotide sequence identity and amino acid sequence similarity of the coat protein region varied from 88% to 99.1% and from 95.1% to 99.6%, respectively. The N-terminal region of coat protein was compared with other members SCMV subgroup and phylogenetic tree was constructed.
comparison with previously analyzed isolates from the GenBank showed 95%–99% sequencesimilarity. The names of the compared isolates and their GenBank access numbers are shown in Table I . The isolates were separated in two distinct subbranches. According to
Authors:Hajnalka Papp, Laila Al-Mutairi, Wassim Chehadeh, Szilvia Farkas, György Lengyel, Ferenc Jakab, Vito Martella, György Szűcs, and Krisztián Bányai
In this study a Kuwaiti camel rotavirus strain, RVA/Camel-wt/KUW/s21/2010/G10P, is characterized by sequencing and phylogenetic analysis. The strain had multiple genes with high nucleotide sequence similarities to ovine and bovine strains (VP2, ≤ 96%; NSP2 and NSP5, ≤ 97%, NSP3, ≤ 94%), or, to porcine strains (VP1, ≤ 89%). Other genes had moderate sequence similarities (VP4, ≤ 87%; VP6, ≤ 81%; VP7, ≤ 82%) with reference strains from ruminants. The NSP4 gene shared limited sequence identity (≤ 71%) with other mammalian and avian rotavirus NSP4 types, and was designated a novel genotype, E15. This study demonstrates genetic diversity in the outer capsid and some backbone genes of an old-world camelid rotavirus strain and uncovers its common evolutionary roots with strains from other ruminants.
Authors:Klára Ács, Zs. Kasza, Gyöngyi Lukács, H. Schwab, and Cs. Vágvölgyi
A genomic library of Mucor circinelloides ATCC 1216b has been constructed in Lambda Fix II vector. The library has an average insert site of 10 kb and covers the genome 12 times. The M. circinelloides gene encoding glyceraldehyde-3-phosphate dehydrogenase (gpd) was isolated from this library by hybridization of the recombinant phage clones with a gpd-specific gene probe generated by PCR reaction. The complete nucleotide sequence encodes a putative polypeptide chain of 339 amino acids interrupted by 3 introns. The predicted amino acid sequence of this gene shows a high degree of sequence similarity to the GPD proteins from other filamentous fungi. The promoter region, containing a consensus TATA and CAAT box and a 298 nucleotid long termination region were also determined.
Authors:Andrea Németh, Barbara Szirányi, Gergely Krett, Endre Janurik, Tünde Kosáros, Ferenc Pekár, Károly Márialigeti, and Andrea Borsodi
Geothermal wells characterized by thermal waters warmer than 30°C can be found in more than 65% of the area of Hungary. The examined thermal wells located nearby Szarvas are used for heating industrial and agricultural facilities because of their relatively high hydrocarbon content. The aim of this study was to reveal the prokaryotic community structure of the water of SZR18, K87 and SZR21 geothermal wells using molecular cloning methods and Denaturing Gradient Gel Electrophoresis (DGGE). Water samples from the outflow pipes were collected in 2012 and 2013. The phylogenetic distribution of archaeal molecular clones was very similar in each sample, the most abundant groups belonged to the genera Methanosaeta, Methanothermobacter and Thermofilum. In contrast, the distribution of bacterial molecular clones was very diverse. Many of them showed the closest sequence similarities to uncultured clone sequences from similar thermal environments. From the water of the SZR18 well, phylotypes closely related to genera Fictibacillus and Alicyclobacillus (Firmicutes) were only revealed, while the bacterial diversity of the K87 well water was much higher. Here, the members of the phyla Thermodesulfobacteria, Proteobacteria, Nitrospira, Chlorobi, OP1 and OPB7 were also detected besides Firmicutes.
Authors:Anna Rusznyák, Gitta Szabó, Beatrix Pollák, Viktória Vágány, and M. Palatinszky
From reed biofilm samples of Kelemen-szék (Kiskunság National Park, KNP) and Nagy-Vadas (Hortobágy National Park, HNP) altogether 260 bacterial isolates were gained after serial dilutions and plating onto different media. Following a primary selection 164 strains were investigated by “traditional” phenotypic tests and clustered by numerical analysis. Fifty-six representative strains were selected to ARDRA and 16S rDNA sequence analysis for identification. Strains were identified as members of genera
Agrobacterium, Paracoccus, Halomonas, Pseudomonas, Bacillus, Planococcus
. The species diversity was also investigated by a cultivation independent method. A clone library was constructed using the community DNA isolated from the biofilm sample of Kelemen-szék. Screening of the 140 bacterial clones resulted in 45 different ARDRA groups. Sequence analysis of the representatives revealed a great phylogenetic diversity. A considerable majority of the clones was affiliated with uncultured bacterial clones (with sequence similarity between 93 and 99%) originating from diverse environmental samples (for example salt marshes, compost or wastewater treatment plants). The DNA sequences of other clones showed the presence of genera
Flavobacterium, Sphingobacterium, Pseudomonas
Authors:Gergely Krett, Viktória Vágány, Judit Makk, Katalin Jáger, Mária Reskóné, Károly Márialigeti, and Andrea Borsodi
Lake Hévíz is the largest natural warm water lake of Europe. The curative mud of the lake comprises volcanic and marsh components although their species composition is hardly known yet. The aim of the present study was to gain information about the distribution and species diversity of bacterial communities inhabiting the sediment of Lake Hévíz using cultivation-based and molecular cloning methods. Samples from two depths and locations were taken in 2004 and 2007. Representatives of the altogether 255 bacterial isolates were affiliated with the phyla Firmicutes, Actinobacteria, Proteobacteria and Bacteroidetes. The most abundant groups belonged to the genus Bacillus (Firmicutes). Many of Lake Hévíz isolates showed the highest sequence similarity to bacteria known to be plant associated or members of normal human microbiota as well as participating in decomposition of highly resistant organic materials. In the three clone libraries, phylotypes belonging to altogether different phyla (Firmicutes, Actinobacteria, Proteobacteria, Bacteroidetes, Cyanobacteria, Chlorobi, Chloroflexi, Deferribacteres, Nitrospirae, Spirochaetes and Verrucomicrobia) were revealed from which members of Gammaproteobacteria and Cyanobacteria proved to be the most abundant. Regardless of the sampling times and methodology used, high spatial heterogeneities of bacterial community structures were characteristic of the sediment of Lake Hévíz.
Recently, four novel genes named Pinb-2, with 57–60% sequence similarity with wild-type allele Pinb-D1a coding for grain-hardness related puroindoline B have been shown to occur on homoeologous group 7 chromosomes in bread wheat (Triticum aestivum). In the present report, T. monococcum ssp. monococcum (Am genome) revealed a Pinb-2 gene with a poly-G tract and an in-frame TAG stop codon at the 5′ terminus of the coding DNA sequence. The stop codon was observed in 53 accessions of different geographic origins, suggesting that Pinb-2 in ‘monococcum’ wheat is unlikely to be expressed. By contrast, the coding DNA sequence of Pinb-2 in T. urartu (Au genome) was found to be 99% identical to its counterpart on chromosome 7AL in bread and durum (T. turgidum ssp. durum) wheat. Moreover, a sequence very similar to “urartu” Pinb-2 was found in tetraploid wheat T. timopheevii and hexaploid wheat T. zhukovskyi. This latter species exhibited an additional Pinb-2 pseudogene inherited from T. monococcum. The results are discussed in relation to the lineage of T. zhukovskyi and the potential role of Pin-b2 on kernel texture.
Powdery mildew (Blumeria graminis f. sp. tritici) is one of the most devastating wheat diseases. The wheat line N9134 contains PmAS846 that was transferred to N9134 from wild emmer wheat, and is still one of the most effective resistance genes in China. A full-length wheat RPM1 gene was obtained by rapid amplification of cDNA ends (RACE) based on the up-regulated probe sequence from differentially expressed transcripts during the N9134 and powdery mildew interaction. The gene was named TaRPM1, and the open reading frame (ORF) is 2721 nucleotides and encodes a polypeptide of 907 amino acids with a predicted isoelectric point of 4.86. Phylogenetic analysis revealed that TaRPM1 was highly homologous on both Aegilops tauschii and Triticum urartu at both the nucleotide and protein level. Using real-time quantitative PCR, the TaRPM1 gene expression level in wheat leaves was found to be sharply up-regulated, while the transcript level was lowly induced in the root and stem. Under the powdery mildew treatment, the transcription profile of TaRPM1 was very strongly expressed at 48 hour post inoculation (hpi), which increased again to 96 hpi and reaching a high level at 120 hpi. Based on sequence similarities and positions, we inferred that the TaRPM1 gene was on wheat chromosome 3D. These results suggested that TaRPM1 plays an important role in the mechanism of innate immunity to infection by the powdery mildew pathogen.
Authors:Z. Huang, H. Long, Y. Wei, P. Qi, Z. Yan, and Y. Zheng
The most abundant seed storage proteins of wheat are gliadins and glutenins. Gliadins, including
types, are normally monomeric proteins and account for about 50% of the gluten proteins. In this study, 55 sequences of
-gliadin genes were obtained from species of
section, the deduced B genome donors of wheat. Despite the high sequence similarities to the known
-gliadin genes, extensive variations were also found. Using the extensive sequence information deposited in database and obtained in this study, a comprehensive classification of the
-gliadin multigene families were performed based on the primary structures and phylogenic analysis. All the
-gliadin genes analyzed could be divided into 2 types, which contain 8 and 9 cysteines, respectively. Type I (with 8 cysteines) and type II (with 9 cysteines) are further classified to 7 and 4 groups, respectively, and several subgroups are also identified. The genes derived from A, B and D genomes of common wheat were clustered distinctly, indicating that there was apparent genomic specificity in
-gliadins genes. Besides the high homology between
-gliadin genes from
species and B genome of wheat, some unique groups or subgroups were also identified in
section, suggesting that it could be considered as a valuable source of
-gliadin genes. The comparison of deduced primary structures of each group and/or subgroup was conducted, from which their evolution and quality properties were also speculated.