Sequence analysis of 16S rRNA, gyrB and catA genes and DNA-DNA hybridization reveal that Rhodococcus jialingiae is a later synonym of Rhodococcus qingshengii

The results of 16S rRNA, gyrB and catA gene sequence comparisons and reasserted DNA–DNA hybridization unambiguously proved that Rhodococcus jialingiae Wang et al. 2010 and Rhodococcus qingshengii Xu et al. 2007 represent a single species. On the basis of priority R. jialingiae must be considered a later synonym of R. qingshengii .</jats:p

Plant polysaccharide degrading enzyme system of Thermobifida cellulosilytica TB100^T revealed by de novo genome project data

Thermobifidas are thermophilic, aerobic, lignocellulose decomposing actinomycetes. The Thermobifida genus includes four species: T. fusca, T. alba, T. cellulosilytica, and T. halotolerans. T. fusca YX is the far best characterized strain of this taxon and several cellulases and hemicellulases have been cloned from it for industrial purposes targeting paper industry, biofuel, and feed applications. Unfortunately, sequence data of such enzymes are almost exclusively restricted to this single species; however, we demonstrated earlier by zymography that other T. alba and T. cellulosilytica strains encode the same enzyme sets. Recently, the advances in whole genome sequencing by the use of next generation genomics platforms accelerated the selection process of valuable hydrolases from uncharacterized bacterial species for cloning purposes. For this purpose T. cellulosilytica TB100T type strain was chosen for de novo genome sequencing. We have assembled the genome of T. cellulosilytica strain TB100T into 168 contigs and 19 scaffolds, with reference length of 4 327 869 bps, 3 589 putative coding sequences, 53 tRNAs, and 4 rRNAs. The analysis of the annotated genome revealed the existence of 27 putative hydrolases belonging to 14 different glycoside hydrolase (GH) families. The investigation of identified, cloned, and heterologously multiple cellulases, mannanases, xylanases, and amylases may result in industrial applications beside gaining useful basic research related information

Proteomics Analysis of Thermoplasma Quinone Droplets.

A novel type of lipid droplet/lipoprotein (LD/LP) particle from Thermoplasma acidophilum has been identified recently, and based on biochemical evidences, it was named Thermoplasma Quinone Droplet (TaQD). The major components of TaQDs are menaquinones, and to some extent polar lipids, and the 153 amino acid long Ta0547 vitellogenin-N domain protein. In this paper, the aim is to identify TaQD proteome components with 1D-SDS-PAGE/LC-MS/MS and cross reference them with Edman degradation. TaQD samples isolated with three different purification methods-column chromatography, immunoprecipitation, and LD ultracentrifugation-are analyzed. Proteins Ta0093, Ta0182, Ta0337, Ta0437, Ta0438, Ta0547, and Ta1223a are identified as constituents of the TaQD proteome. The majority of these proteins is uncharacterized and has low molecular weight, and none of them is predicted to take part in lipid metabolism. Bioinformatics analyses does not predict any interaction between these proteins, however, there are indications of interactions with proteins taking part in lipid metabolism. Whether if TaQDs provide platform for lipid metabolism and the interactions between TaQD proteins and lipid metabolism proteins occur in the reality remain for further studies. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

Mycotoxin-degradation profile of Rhodococcus strains

Mycotoxins are secondary fungal metabolites that may have mutagenic, carcinogenic, cytotoxic and endocrine disrupting effects. These substances frequently contaminate agricultural commodities despite efforts to prevent them, so successful detoxification tools are needed. The application of microorganisms to biodegrade mycotoxins is a novel strategy that shows potential for application in food and feed processing. In this study we investigated the mycotoxin degradation ability of thirty-two Rhodococcus strains on economically important mycotoxins: aflatoxin B-1, zearalenone, fumonisin B-1, T2 toxin and ochratoxin A, and monitored the safety of aflatoxin B-1 and zearalenone degradation processes and degradation products using previously developed toxicity profiling methods. Moreover, experiments were performed to analyse multi-mycotoxin-degrading ability of the best toxin degrader/detoxifier strains on aflatoxin B-1, zearalenone and T2 toxin mixtures. This enabled the safest and the most effective Rhodococcus strains to be selected, even for multi-mycotoxin degradation. We concluded that several Rhodococcus species are effective in the degradation of aromatic mycotoxins and their application in mycotoxin biodetoxification processes is a promising field of biotechnology. (C) 2013 Elsevier B.V. All rights reserved

Enhancing recombinant protein solubility with ubiquitin-like small archeal modifying protein fusion partners

A variety of protein expression tags with different biochemical properties has been used to enhance the yield and solubility of recombinant proteins. Ubiquitin, SUMO (small ubiquitin-like modifier) and prokaryotic ubiquitin like MoaD (molybdopterin synthase, small subunit) fusion tags are getting more popular because of their small size. In this paper we report on the use of ubiquitin-like small archaeal modifier proteins (SAMPs) as fusion tags since they proved to increase expression yield, stability and solubility in our experiments. Equally important, they did not co-purify with proteins of the expression host and there was information that their specific JAB1/MPN/Mov34 metalloenzyme (JAMM) protease can recognize the C-terminal VSGG sequence when SAMPs fused, either branched or linearly to target proteins, and cleave it specifically. SAMPs and JAMM proteases from Haloferax volcanii, Thermoplasma acidophilum, Methanococcoides burtonii and Nitrosopumilus maritimus were selected, cloned, expressed heterologously in Escherichia coli and tested as fusion tags and cleaving proteases, respectively. Investigated SAMPs enhanced protein expression and solubility on a wide scale. T. acidophilum SAMPs Ta0895 and Ta01019 were the best performing tags and their effect was comparable to the widely used maltose binding protein (MBP) and N utilization substance protein A (NusA) tags. Moreover, H. volcanii SAMP Hvo_2619 contribution was mediocre, whereas M. burtonii Mbur_1415 could not be expressed. Out of four investigated JAMM proteases, only Hvo_2505 could cleave fusion tags. Interestingly, it was found active not only on its own partner substrate Hvo_2619, but it also cleaved off Ta0895. (C) 2015 Elsevier B.V. All rights reserved

Isolation and Detailed Characterisation of the First Sterigmatocystin Hyperproducer Mould Strain in Hungary

Aspergillus strains were isolated from Hungarian mills in order to get information on the appearance of sterigmatocystin (ST) producing moulds, whose presence has never been demonstrated in Hungary. Fungal isolates were classified into nine morphotypes, sections Nigri, Nidulantes, Versicolores (two morphotypes), Circumdati, Flavi (two morphotypes), Clavati and Terrei by classical mycological assays. ST producing strains could be classified into section Versicolores. ST production of the isolates was assessed by liquid and solid phase growth experiments and compared to ST producing reference strains: Aspergillus pepii SzMC 22332, Aspergillus versicolor SzMC 22333, Aspergillus griseoaurantiacus SzMC 22334 and Aspergillus nidulans RDIT9.32. Four of our isolates marked as Km11, Km14, Km26 and Km31 showed ST production in liquid medium. ST production on solid phase corn grit substrate was measured after three weeks of incubation, and Km26 isolate proved to be the most prominent with a toxin concentration of 277.1 μg g−1, surpassing all reference strains. The toxin-producing ability of Km26 isolate was also tested in a field experiment, where corn was infected. By the end of the experiment, ST level of 19.56 μg kg−1 was measured in infected corn. Molecular taxonomic identification of the Km26 strain was performed using internal transcribed spacer (ITS), calmodulin and tubulin sequence analyses. Based on these studies, strain Km26 was identified as Aspergillus creber. Here we report that an ST-producing A. creber strain has appeared in Hungary, and the Km26 strain is the first known extreme ST-producing mould in this country. As a result of climate change, aflatoxin B1 producing Aspergillus flavus strains have appeared in Hungary in the last decade. As strain Km26 is the only A. creber isolate in Hungary so far, there is no sign of mass prevalence, and due to the lower temperature optimum of the species compared to A. flavus, its appearance is probably not related to climate change