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https://www.readbyqxmd.com/read/29152711/the-burst-phase-folding-intermediate-of-ribonuclease-h-changes-conformation-over-evolutionary-history
#1
Shion A Lim, Susan Marqusee
The amino acid sequence encodes the energy landscape of a protein. Therefore, we expect evolutionary mutations to change features of the protein energy landscape, including the conformations adopted by a polypeptide as it folds to its native state. Ribonucleases H (RNase H) from Escherichia coli and Thermus thermophilus both fold via a partially folded intermediate in which the core region of the protein (helices A-D and strands 4-5) is structured. Strand 1, however, uniquely contributes to the T. thermophilus RNase H folding intermediate (Icore+1 ), but not the E...
November 20, 2017: Biopolymers
https://www.readbyqxmd.com/read/29150497/low-molecular-weight-thiols-and-thioredoxins-are-important-players-in-hg-ii-resistance-in-thermus-thermophilus-hb27
#2
J Norambuena, Y Wang, T Hanson, J M Boyd, T Barkay
Mercury (Hg), one of the most toxic and widely distributed heavy metals, has a high affinity for thiol groups. Thiol groups reduce and sequester Hg. Therefore, low molecular weight and protein thiols may be important cell components used in Hg resistance. To date, the role of low molecular weight thiols in Hg-detoxification remains understudied. The mercury resistance (mer) operon of Thermus thermophilus suggests an evolutionary link between Hg(II) resistance and low molecular weight thiol metabolism. This mer operon encodes for an enzyme involved in methionine biosynthesis, Oah...
November 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29118742/diets-alter-the-gut-microbiome-of-crocodile-lizards
#3
Hai-Ying Jiang, Jing-E Ma, Juan Li, Xiu-Juan Zhang, Lin-Miao Li, Nan He, Hai-Yang Liu, Shu-Yi Luo, Zheng-Jun Wu, Ri-Chou Han, Jin-Ping Chen
The crocodile lizard is a critically endangered reptile, and serious diseases have been found in this species in recent years, especially in captive lizards. Whether these diseases are caused by changes in the gut microbiota and the effect of captivity on disease remains to be determined. Here, we examined the relationship between the gut microbiota and diet and disease by comparing the fecal microbiota of wild lizards with those of sick and healthy lizards in captivity. The gut microbiota in wild crocodile lizards was consistently dominated by Proteobacteria (∼56...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29106607/rnomics-of-thermus-themophilus-hb8-by-dna-microarray-and-next-generation-sequencing
#4
Gota Kawai, Yuri Aoki, Maina Otsu, Naomi Koike, Gen-Ichi Sampei
By using the data obtained by the DNA microarray analysis for the intergenic regions applied to RNA samples extracted from Thermus thermophilus HB8, seven small non-coding RNAs, TtR-1 to TtR-7, were found to be expressed in the cells growing in rich and/or minimal media. By analysing the time course of the expression for the cell growth in combination with the sequence comparison to the known RNAs, two RNAs, TtR-1 and TtR-2, are suggested to be riboswitches. The existence of the seven RNAs and the exact sequence and length, ranging 77-284 nt, were confirmed by the next-generation sequencing...
July 4, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/29097207/site-specific-aptamer-inhibitors-of-thermus-rna-polymerase
#5
Nataliya Miropolskaya, Andrey Feklistov, Vadim Nikiforov, Andrey Kulbachinskiy
Bacterial RNA polymerase (RNAP) is an RNA-synthesizing molecular machine and a target for antibiotics. In transcription, RNAP can interact with DNA sequence-specifically, during promoter recognition by the σ-containing holoenzyme, or nonspecifically, during productive RNA elongation by the core RNAP. We describe high-affinity single-stranded DNA aptamers that are specifically recognized by the core RNAP from Thermus aquaticus. The aptamers interact with distinct epitopes inside the RNAP main channel, including the rifamycin pocket, and sense the binding of other RNAP ligands such as rifamycin and the σ(A) subunit...
October 30, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29079773/community-structure-of-gut-bacteria-of-dendroctonus-armandi-coleoptera-curculionidae-scolytinae-larvae-during-overwintering-stage
#6
Juan Wang, Hui Chen, Ming Tang
Survival rate at low temperature becomes a crucial strategy since temperature change often leads to fluctuations in the insect population. Microbes play important roles in the process of resisting low temperature. In this study, we analyzed gut bacterial communities from Chinese white pine beetle Dendroctonus armandi which remained overwintering process under natural conditions from October 2015 to January 2016, monthly, in the Qinling Mountains, Shaanxi, China using Illumina MiSeq sequencing. A total of 835,227 high-quality sequences and 48 singleton operational taxonomic units were obtained...
October 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29067010/nitric-oxide-accumulation-the-evolutionary-trigger-for-phytopathogenesis
#7
Margarida M Santana, Juan M Gonzalez, Cristina Cruz
Many publications highlight the importance of nitric oxide (NO) in plant-bacteria interactions, either in the promotion of health and plant growth or in pathogenesis. However, the role of NO in the signaling between bacteria and plants and in the fate of their interaction, as well as the reconstruction of their interactive evolution, remains largely unknown. Despite the complexity of the evolution of life on Earth, we explore the hypothesis that denitrification and aerobic respiration were responsible for local NO accumulation, which triggered primordial antagonistic biotic interactions, namely the first phytopathogenic interactions...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29066751/revealing-the-gut-bacteriome-of-dendroctonus-bark-beetles-curculionidae-scolytinae-diversity-core-members-and-co-evolutionary-patterns
#8
Juan Alfredo Hernández-García, Carlos Iván Briones-Roblero, Flor N Rivera-Orduña, Gerardo Zúñiga
Dendroctonus bark beetles comprise 20 taxonomically recognized species, which are one of the most destructive pine forest pests in North and Central America, and Eurasia. The aims of this study were to characterize the gut bacterial diversity, to determine the core bacteriome and to explore the ecological association between these bacteria and bark beetles. A total of five bacterial phyla were identified in the gut of 13 Dendroctonus species; Proteobacteria was the most abundant, followed by Firmicutes, Fusobacteria, Actinobacteria and Deinococcus-Thermus...
October 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29063287/characterization-of-a-mildly-alkalophilic-and-thermostable-recombinant-thermus-thermophilus-laccase-with-applications-in-decolourization-of-dyes
#9
Arpana Kumari, Nitin Kishor, Purnananda Guptasarma
OBJECTIVE: To examine the potential for applications of TthLAC, a monomeric (~ 53 kDa) laccase encoded by the genome of Thermus thermophilus (strain HB 27) which can be produced at low cost in Escherichia coli. RESULT: Functional, thermostable and mildly alkalophilic TthLAC of high purity (> 90%) was produced through simple heating of suspended (TthLAC overexpressing) E.coli cells at 65 °C. For reactions of short duration (< 1 h) the temperature for optimal activity is ~ 90 °C...
October 23, 2017: Biotechnology Letters
https://www.readbyqxmd.com/read/29048593/fidelity-of-rna-templated-end-joining-by-chlorella-virus-dna-ligase-and-a-novel-ilock-assay-with-improved-direct-rna-detection-accuracy
#10
Tomasz Krzywkowski, Mats Nilsson
Ligation-based nucleic acid detection methods are primarily limited to DNA, since they exhibit poor performance on RNA. This is attributed to reduced end-joining efficiency and/or fidelity of ligases. Interestingly, chlorella virus DNA ligase (PBCV-1 DNA ligase) has recently been shown to possess high RNA-templated DNA end-joining activity; however, its fidelity has not yet been systematically evaluated. Herein, we characterized PBCV-1 ligase for its RNA-templated end-joining fidelity at single base mismatches in 3' and 5' DNA probe termini and found an overall limited end-joining fidelity...
October 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29040308/thermostable-proteins-bioprocesses-the-activity-of-restriction-endonuclease-methyltransferase-from-thermus-thermophilus-rm-tthhb27i-cloned-in-escherichia-coli-is-critically-affected-by-the-codon-composition-of-the-synthetic-gene
#11
Daria Krefft, Aliaksei Papkov, Agnieszka Zylicz-Stachula, Piotr M Skowron
Obtaining thermostable enzymes (thermozymes) is an important aspect of biotechnology. As thermophiles have adapted their genomes to high temperatures, their cloned genes' expression in mesophiles is problematic. This is mainly due to their high GC content, which leads to the formation of unfavorable secondary mRNA structures and codon usage in Escherichia coli (E. coli). RM.TthHB27I is a member of a family of bifunctional thermozymes, containing a restriction endonuclease (REase) and a methyltransferase (MTase) in a single polypeptide...
2017: PloS One
https://www.readbyqxmd.com/read/29037779/-13-c-metabolic-flux-analysis-of-three-divergent-extremely-thermophilic-bacteria-geobacillus-sp-lc300-thermus-thermophilus-hb8-and-rhodothermus-marinus-dsm-4252
#12
Lauren T Cordova, Robert M Cipolla, Adti Swarup, Christopher P Long, Maciek R Antoniewicz
Thermophilic organisms are being increasingly investigated and applied in metabolic engineering and biotechnology. The distinct metabolic and physiological characteristics of thermophiles, including broad substrate range and high uptake rates, coupled with recent advances in genetic tool development, present unique opportunities for strain engineering. However, poor understanding of the cellular physiology and metabolism of thermophiles has limited the application of systems biology and metabolic engineering tools to these organisms...
October 14, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/28980143/nmr-assignments-of-the-n-terminal-domain-of-staphylococcus-aureus-hibernation-promoting-factor-sahpf
#13
Konstantin S Usachev, Rustam Kh Ayupov, Shamil Z Validov, Iskander Sh Khusainov, Marat M Yusupov
Staphylococcus aureus: hibernation-promoting factor (SaHPF) is a 22.2 kDa stationary-phase protein that binds to the ribosome and turns it to the inactive form favoring survival under stress. Sequence analysis has shown that this protein is combination of two homolog proteins obtained in Escherichia coli-ribosome hibernation promoting factor (HPF) (11,000 Da) and ribosome modulation factor RMF (6500 Da). Binding site of E. coli HPF on the ribosome have been shown by X-ray study of Thermus thermophilus ribosome complex...
October 4, 2017: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/28960712/a-high-throughput-mass-spectrometry-based-assay-for-identifying-the-biochemical-functions-of-putative-glycosidases
#14
Tianyuan Peng, Gabe Nagy, Jonathan C Trinidad, Joy Marie Jackson, Nicola L B Pohl
The most commonly employed glycosidase assays rely on bulky ultraviolet or fluorescent tags at the anomeric position in potential carbohydrate substrates, thereby limiting the utility of these assays for broad substrate characterization. Here we report a qualitative mass spectrometry-based glycosidase assay amenable to high-throughput screening for the identification of the biochemical functions of putative glycosidases. The assay utilizes a library of methyl glycosides and is demonstrated on a high-throughput robotic liquid handling system for enzyme substrate screening...
September 27, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28955971/a-specific-single-stranded-dna-induces-a-distinct-conformational-change-in-the-nucleoid-associated-protein-hu
#15
Yuya Nishida, Teppei Ikeya, Tsutomu Mikawa, Jin Inoue, Yutaka Ito, Yasunori Shintani, Ryoji Masui, Seiki Kuramitsu, Seiji Takashima
In prokaryotic cells, genomic DNA forms an aggregated structure with various nucleoid-associated proteins (NAPs). The functions of genomic DNA are cooperatively modulated by NAPs, of which HU is considered to be one of the most important. HU binds double-stranded DNA (dsDNA) and serves as a structural modulator in the genome architecture. It plays important roles in diverse DNA functions, including replication, segregation, transcription and repair. Interestingly, it has been reported that HU also binds single-stranded DNA (ssDNA) regardless of sequence...
December 2016: Biochemistry and Biophysics Reports
https://www.readbyqxmd.com/read/28955773/indispensable-residue-for-uridine-binding-in-the-uridine-cytidine-kinase-family
#16
Fumiaki Tomoike, Noriko Nakagawa, Kenji Fukui, Takato Yano, Seiki Kuramitsu, Ryoji Masui
Uridine-cytidine kinase (UCK), including human UCK2, are a family of enzymes that generally phosphorylate both uridine and cytidine. However, UCK of Thermus thermophilus HB8 (ttCK) phosphorylates only cytidine. This cytidine-restricted activity is thought to depend on Tyr93, although the precise mechanism remains unresolved. Exhaustive mutagenesis of Tyr93 in ttCK revealed that the uridine phosphorylation activity was restored only by replacement of Tyr93 with His or Gln. Replacement of His117 in human UCK2, corresponding to residue Tyr93 in ttCK, by Tyr resulted in a loss of uridine phosphorylation activity...
September 2017: Biochemistry and Biophysics Reports
https://www.readbyqxmd.com/read/28941838/study-of-ciprofloxacin-biodegradation-by-a-thermus-sp-isolated-from-pharmaceutical-sludge
#17
Lan-Jia Pan, Jie Li, Chun-Xing Li, Xiao-da Tang, Guang-Wei Yu, Yin Wang
Ciprofloxacin (CIP) is an antibiotic drug frequently detected in manure compost and is difficult to decompose at high temperatures, resulting in a potential threat to the environment. Microbial degradation is an effective and environmentally friendly method to degrade CIP. In this study, a thermophilic bacterium that can degrade CIP was isolated from sludge sampled from an antibiotics pharmaceutical factory. This strain is closely related to Thermus thermophilus based on 16S rRNA gene sequence analysis and is designated C419...
September 7, 2017: Journal of Hazardous Materials
https://www.readbyqxmd.com/read/28938870/evaluation-of-prokaryotic-diversity-of-five-hot-springs-in-eritrea
#18
Amanuel M Ghilamicael, Nancy L M Budambula, Sylvester E Anami, Tadesse Mehari, Hamadi I Boga
BACKGROUND: Total community rDNA was used to determine the diversity of bacteria and archaea from water, wet sediment and microbial mats samples of hot springs in the Eastern lowlands of Eritrea. The temperatures of the springs range from 49.5 °C to 100 °C while pH levels varied from 6.97 to 7.54. Akwar and Maiwooi have high carbonate levels. The springs near the seashore, Garbanabra and Gelti, are more saline with higher levels of sodium and chlorides. Elegedi, situated in the Alid volcanic area, has the highest temperature, iron and sulfate concentrations...
September 22, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28916375/bacterial-community-in-ancient-permafrost-alluvium-at-the-mammoth-mountain-eastern-siberia
#19
Anatoli Brouchkov, Marsel Kabilov, Svetlana Filippova, Olga Baturina, Victor Rogov, Valery Galchenko, Andrey Mulyukin, Oksana Fursova, Gennady Pogorelko
Permanently frozen (approx. 3.5Ma) alluvial Neogene sediments exposed in the Aldan river valley at the Mammoth Mountain (Eastern Siberia) are unique, ancient, and poorly studied permafrost environments. So far, the structure of the indigenous bacterial community has remained unknown. Use of 16S metagenomic analysis with total DNA isolation using DNA Spin Kit for Soil (MO-Bio) and QIAamp DNA Stool Mini Kit (Qiagen) has revealed the major and minor bacterial lineages in the permafrost alluvium sediments. In sum, 61 Operational Taxonomic Units (OTUs) with 31,239 reads (Qiagen kit) and 15,404 reads (Mo-Bio kit) could be assigned to the known taxa...
December 15, 2017: Gene
https://www.readbyqxmd.com/read/28911108/the-third-restriction-modification-system-from-thermus-aquaticus-yt-1-solving-the-riddle-of-two-taqii-specificities
#20
Piotr M Skowron, Brian P Anton, Edyta Czajkowska, Joanna Zebrowska, Ewa Sulecka, Daria Krefft, Joanna Jezewska-Frackowiak, Olga Zolnierkiewicz, Malgorzata Witkowska, Richard D Morgan, Geoffrey G Wilson, Alexey Fomenkov, Richard J Roberts, Agnieszka Zylicz-Stachula
Two restriction-modification systems have been previously discovered in Thermus aquaticus YT-1. TaqI is a 263-amino acid (aa) Type IIP restriction enzyme that recognizes and cleaves within the symmetric sequence 5'-TCGA-3'. TaqII, in contrast, is a 1105-aa Type IIC restriction-and-modification enzyme, one of a family of Thermus homologs. TaqII was originally reported to recognize two different asymmetric sequences: 5'-GACCGA-3' and 5'-CACCCA-3'. We previously cloned the taqIIRM gene, purified the recombinant protein from Escherichia coli, and showed that TaqII recognizes the 5'-GACCGA-3' sequence only...
September 6, 2017: Nucleic Acids Research
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