158,196 results match your criteria conserved sequences

Adaptation of a parasitic lifestyle by gronovii Willd. ex Roem. & Schult.: large scale gene deletion, conserved gene orders, and low intraspecific divergence.

Mitochondrial DNA B Resour 2021 Apr 20;6(4):1475-1482. Epub 2021 Apr 20.

Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, P. R. China.

Willd. ex Roem. & Schult. Read More

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The complete chloroplast genome of : molecular structures and comparative analysis.

Mitochondrial DNA B Resour 2021 Apr 19;6(4):1431-1439. Epub 2021 Apr 19.

Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China.

is a common ornamental arbor in the genus (family Rosaceae). Here, we sequenced and assembled the complete plastome of using the next-generation DNA sequencing technology. And we then compared it with nine species using a range of bioinformatics software tools. Read More

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Molecular characterization of two highly divergent Iranian johnsongrass mosaic virus isolates from .

Virusdisease 2021 Mar 7;32(1):155-160. Epub 2021 Mar 7.

Department of Plant Pathology, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran.

Iranian johnsongrass mosaic virus (IJMV, genus , family ) is one of the most prevalent viruses causing maize mosaic disease in Iran. In this study, the complete genomes (9,618 and 9,543 nucleotides) of two highly divergent IJMV isolates (Maz2 and Maz3) were obtained from the metagenomic analysis of RNAs using Illumina sequencing. The genome contained a single open reading frame (9,165 nucleotides) encoding a polyprotein of 3,054 amino acids, flanked by a 5'-untranslated region (UTR) of 216 and 143 nucleotides and a 3'-UTR of 237 and 235 nucleotides. Read More

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A putative novel starch-binding domain revealed by in silico analysis of the N-terminal domain in bacterial amylomaltases from the family GH77.

3 Biotech 2021 May 21;11(5):229. Epub 2021 Apr 21.

Department of Biology, Faculty of Natural Sciences, University of SS. Cyril and Methodius, Nám. J. Herdu 2, 91701 Trnava, Slovakia.

The family GH77 contains 4-α-glucanotransferase acting on α-1,4-glucans, known as amylomaltase in prokaryotes and disproportionating enzyme in plants. A group of bacterial GH77 members, represented by amylomaltases from and , possesses an N-terminal extension that forms a distinct immunoglobulin-like fold domain, of which no function has been identified. Here, in silico analysis of 100 selected sequences of N-terminal domain homologues disclosed several well-conserved residues, among which Tyr108 ( amylomaltase numbering) may be involved in α-glucan binding. Read More

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Identification and characterization of alkaline phosphatase gene in PCC7806.

3 Biotech 2021 May 16;11(5):218. Epub 2021 Apr 16.

School of Life Sciences, Nanjing Normal University, Nanjing, 210023 China.

PhoX is an extracellular alkaline phosphatase that is widely found in cyanobacteria and plays an important role in the conversion of extracellular organophosphorus into soluble inorganic phosphorus. However, the gene has not yet been experimentally confirmed to exist in bloom-forming species. In this study, we identified a putative gene (GenBank accession no. Read More

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Molecular characterization of cathelicidin in tiger frog (Hoplobatrachus rugulosus): Antimicrobial activity and immunomodulatory activity.

Comp Biochem Physiol C Toxicol Pharmacol 2021 May 6:109072. Epub 2021 May 6.

College of Ecology, Lishui University, Lishui 323000, China. Electronic address:

Cathelicidins are an important antimicrobial peptide family and are expressed in many different vertebrates. They play an important role in the innate immune system of the host. However, amphibian cathelicidins are poorly understood. Read More

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Crystal structure of restriction endonuclease Kpn2I of CCGG-family.

Biochim Biophys Acta Gen Subj 2021 May 6:129926. Epub 2021 May 6.

Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania. Electronic address:

Background: Restriction endonucleases belong to prokaryotic restriction-modification systems, that protect host cells from invading DNA. Type II restriction endonucleases recognize short 4-8 bp sequences in the target DNA and cut both DNA strands producing double strand breaks. Type II restriction endonuclease Kpn2I cleaves 5'-T/CCGGA DNA sequence ("/" marks the cleavage position). Read More

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Regulation of GC box activity by 8-oxoguanine.

Redox Biol 2021 Apr 30;43:101997. Epub 2021 Apr 30.

Unit "Responses to DNA Lesions", Institute of Toxicology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, 55131, Germany; Institute of Nutritional Science, University of Jena, Jena, 07743, Germany. Electronic address:

The oxidation-induced DNA modification 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) was recently implicated in the activation and repression of gene transcription. We aimed at a systematic characterisation of the impacts of 8-oxodG on the activity of a GC box placed upstream from the RNA polymerase II core promoter. With the help of reporters carrying single synthetic 8-oxodG residues at four conserved G:C base pairs (underlined) within the 5'-TGGGCGGAGC-3' GC box sequence, we identified two modes of interference of 8-oxodG with the promoter activity. Read More

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EHD3 positively regulated by NR5A1 participates in testosterone synthesis via endocytosis.

Life Sci 2021 May 5:119570. Epub 2021 May 5.

NHC Key Lab of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), School of Pharmacy, Fudan University, Shanghai 200032, China; NHC Key Lab of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Fudan University, Shanghai 200032, China. Electronic address:

Aims: Increasing evidence has shown that hormone secretion is regulated by endocytosis. Eps15 homology domain-containing protein 3 (EHD3) is an endocytic-trafficking regulatory protein, but whether EHD3 is associated with testosterone secretion is not clear. This work aims to explore the role of EHD3 in testosterone synthesis. Read More

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BENZ WS: the Bologna ENZyme Web Server for four-level EC number annotation.

Nucleic Acids Res 2021 May 8. Epub 2021 May 8.

Biocomputing Group, Department of Pharmacy and Biotechnologies, University of Bologna, Italy.

The Bologna ENZyme Web Server (BENZ WS) annotates four-level Enzyme Commission numbers (EC numbers) as defined by the International Union of Biochemistry and Molecular Biology (IUBMB). BENZ WS filters a target sequence with a combined system of Hidden Markov Models, modelling protein sequences annotated with the same molecular function, and Pfams, carrying along conserved protein domains. BENZ returns, when successful, for any enzyme target sequence an associated four-level EC number. Read More

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Targeting the conserved stem loop 2 motif in the SARS-CoV-2 genome.

J Virol 2021 May 7. Epub 2021 May 7.

Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, U.K.

RNA structural elements occur in numerous single stranded (+)-sense RNA viruses. The stem-loop 2 motif (s2m) is one such element with an unusually high degree of sequence conservation, being found in the 3' UTR in the genomes of many astroviruses, some picornaviruses and noroviruses, and a variety of coronaviruses, including SARS-CoV and SARS-CoV-2. The evolutionary conservation and its occurrence in all viral subgenomic transcripts implicates a key role of s2m in the viral infection cycle. Read More

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Immunogenicity and structural efficacy of P41 of Plasmodium sp. as potential cross-species blood-stage malaria vaccine.

Comput Biol Chem 2021 Apr 24;92:107493. Epub 2021 Apr 24.

Department of Bioinformatics, School of Life Sciences, Indonesia International Institute for Life Sciences, Jakarta, Indonesia. Electronic address:

Vaccine based strategies offer a promising future in malaria control by generating protective immunity against natural infection. However, vaccine development is hindered by the Plasmodium sp. genetic diversity. Read More

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Myomixer is expressed during embryonic and post-larval hyperplasia, muscle regeneration and differentiation of myoblats in rainbow trout (Oncorhynchus mykiss).

Gene 2021 May 4:145688. Epub 2021 May 4.

INRAE, UR1037 Laboratory of Fish Physiology and Genomics, 35000 Rennes, France. Electronic address:

In contrast to mice or zebrafish, trout exhibits post-larval muscle growth through hypertrophy and formation of new myofibers (hyperplasia). The muscle fibers are formed by the fusion of mononucleated cells (myoblasts) regulated by several muscle-specific proteins such as Myomaker or Myomixer. In this work, we identified a unique gene encoding a Myomixer protein of 77 amino acids (aa) in the trout genome. Read More

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-like genome architecture among carbapenemase-producing and in the Netherlands.

Microb Genom 2021 May;7(5)

Centre for Infectious Diseases Research, Diagnostics and Laboratory Surveillance, Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands.

Carbapenem-hydrolysing enzymes belonging to the OXA-48-like group are encoded by -like alleles and are abundant among in the Netherlands. Therefore, the objective here was to investigate the characteristics, gene content and diversity of the -like carrying plasmids and chromosomes of and collected in the Dutch national surveillance from 2014 to 2019 in comparison with genome sequences from 29 countries. A combination of short-read genome sequencing with long-read sequencing enabled the reconstruction of 47 and 132 complete -like plasmids for and , respectively. Read More

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Insights into the acquisition of the island and production of colibactin in the population.

Microb Genom 2021 May;7(5)

IRSD, INSERM, Université de Toulouse, INRAE, ENVT, UPS, Toulouse, France.

The island codes for the enzymes necessary for synthesis of the genotoxin colibactin, which contributes to the virulence of strains and is suspected of promoting colorectal cancer. From a collection of 785 human and bovine isolates, we identified 109 strains carrying a highly conserved island, mostly from phylogroup B2, but also from phylogroups A, B1 and D. Different scenarios of acquisition were deduced from whole genome sequence and phylogenetic analysis. Read More

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Inferring Core Genome Phylogenies for Bacteria.

Methods Mol Biol 2021 ;2242:59-68

Center for Computational and Theoretical Biology, Biocenter, University of Würzburg, Würzburg, Germany.

Due to the increasing availability of public bacterial genome data and cost efficiency of novel bacterial strain sequencing, phylogenetic analyses based on more than a single or few marker genes have become feasible. In this method protocol, we describe the complete bioinformatic workflow from raw genomic data to final phylogenetic analyses based on 107 conserved single copy genes. This approach can be used to perform phylogenetic reconstructions with high resolution on strain level or across taxa spanning different clades of the bacterial tree of life. Read More

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January 2021

Uncovering the first occurrence of Tilapia parvovirus in Thailand in tilapia during co-infection with Tilapia tilapinevirus.

Transbound Emerg Dis 2021 May 7. Epub 2021 May 7.

Department of Veterinary Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand.

The recently-discovered Tilapia parvovirus (TiPV) was the first Parvovirus confirmed to infect fish, causing mortality outbreaks in farmed adult Nile tilapia in China. Severe mortality outbreaks caused by Tilapia tilapinevirus (TiLV) to farmed tilapia in Thailand revealed the concomitant occurrence of TiPV. Out of ten fish farms screened, TiPV was detected in one site rearing juvenile red hybrid tilapia. Read More

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Genetic Diversity of Recent Infectious Bursal Disease Viruses Isolated From Vaccinated Poultry Flocks in Malaysia.

Front Vet Sci 2021 20;8:643976. Epub 2021 Apr 20.

Department of Veterinary Clinical Studies, Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Malaysia.

Vaccination is an essential component in controlling infectious bursal disease (IBD), however, there is a lack of information on the genetic characteristics of a recent infectious bursal disease virus (IBDV) that was isolated from IBD vaccinated commercial flocks in Malaysia. The present study investigated 11 IBDV isolates that were isolated from commercial poultry farms. The isolates were detected using reverse transcription-polymerase chain reaction (RT-PCR) targeting the hypervariable region (HVR) of VP2. Read More

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CTCF As an Example of DNA-Binding Transcription Factors Containing Clusters of C2H2-Type Zinc Fingers.

Acta Naturae 2021 Jan-Mar;13(1):31-46

Institute of Gene Biology RAS, Moscow, 119334 Russia.

In mammals, most of the boundaries of topologically associating domains and all well-studied insulators are rich in binding sites for the CTCF protein. According to existing experimental data, CTCF is a key factor in the organization of the architecture of mammalian chromosomes. A characteristic feature of the CTCF is that the central part of the protein contains a cluster consisting of eleven domains of C2H2-type zinc fingers, five of which specifically bind to a long DNA sequence conserved in most animals. Read More

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Evidence of Recombination Suppression Blocks on the Y Chromosome of Date Palm ().

Front Plant Sci 2021 20;12:634901. Epub 2021 Apr 20.

Genomics Laboratory, Weill Cornell Medicine in Qatar, Doha, Qatar.

The genus includes the fruit producing date palm tree among 14 species that are all dioecious. Females produce the fruit that are high in sugar content and used in multiple countries ranging from North Africa to South Asia, especially from the , , and species. While females produce the fruit, understanding of the genetic basis of sex control only began recently. Read More

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Expanding Diversity of Single-Strand Annealing Proteins: A Putative Role of Bacteriophage-Host Arms Race.

Front Microbiol 2021 20;12:644622. Epub 2021 Apr 20.

Institute of Biochemistry and Biophysics PAS, Warsaw, Poland.

Bacteriophage-encoded single strand annealing proteins (SSAPs) are recombinases which can substitute the classical, bacterial RecA and manage the DNA metabolism at different steps of phage propagation. SSAPs have been shown to efficiently promote recombination between short and rather divergent DNA sequences and were exploited for genetic engineering mainly in Gram-negative bacteria. In opposition to the conserved and almost universal bacterial RecA protein, SSAPs display great sequence diversity. Read More

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Widespread divergent transcription from bacterial and archaeal promoters is a consequence of DNA-sequence symmetry.

Nat Microbiol 2021 May 6. Epub 2021 May 6.

Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, UK.

Transcription initiates at promoters, DNA regions recognized by a DNA-dependent RNA polymerase. We previously identified horizontally acquired Escherichia coli promoters from which the direction of transcription was unclear. In the present study, we show that more than half of these promoters are bidirectional and drive divergent transcription. Read More

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Phosphorylation of the WH2 domain in yeast Las17/WASP regulates G-actin binding and protein function during endocytosis.

Sci Rep 2021 May 6;11(1):9718. Epub 2021 May 6.

Department of Biomedical Science, Firth Court, University of Sheffield, Sheffield, S10 2TN, UK.

Actin nucleation is the key rate limiting step in the process of actin polymerization, and tight regulation of this process is critical to ensure actin filaments form only at specific times and at defined regions of the cell. WH2 domains are short sequence motifs found in many different actin binding proteins including WASP family proteins which regulate the actin nucleating complex Arp2/3. In this study we reveal a phosphorylation site, Serine 554, within the WH2 domain of the yeast WASP homologue Las17. Read More

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Comprehensive molecular dissection of TIFY Transcription factors reveal their dynamic responses to biotic and abiotic stress in wheat (Triticum aestivum L.).

Sci Rep 2021 May 6;11(1):9739. Epub 2021 May 6.

Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, 835215, Jharkhand, India.

The plant specific TIFY (previously known as ZIM) transcription factor (TF) family plays crucial roles in cross talk between Jasmonic Acid and other phytohormones like gibberellins, salicylic acid, abscisic acid, auxin, and ethylene signaling pathways. Wheat yield is severely affected by rust diseases and many abiotic stresses, where different phytohormone signaling pathways are involved. TIFYs have been studied in many plants yet reports describing their molecular structure and function in wheat are lacking. Read More

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Characterization of a novel carboxylesterase with catalytic activity toward di(2-ethylhexyl) phthalate from a soil metagenomic library.

Sci Total Environ 2021 Apr 21;785:147260. Epub 2021 Apr 21.

Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China. Electronic address:

A novel carboxylesterase gene estyz5 was isolated from a soil metagenomic library. The recombinant enzyme EstYZ5 is 298 amino acids in length with a predicted molecular weight of 32 kDa. Sequence alignment and phylogenetic analysis revealed that EstYZ5 belongs to the hormone-sensitive lipase (HSL) family with a deduced catalytic triad of Ser144-Glu238-His268. Read More

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Toxicon research paper Structural and bioinformatic analyses of Azemiops venom serine proteases reveal close phylogeographic relationships to pitvipers from eastern China and the New World.

Toxicon 2021 May 3. Epub 2021 May 3.

Institute of Biological Chemistry,Academia Sinica,Taipei, Taiwan.

The semi-fossil and pit-less Azemiops feae is possibly the most primitive crotalid species. Here, we have cloned and sequenced cDNAs encoding four serine proteases (vSPs) from the venom glands of Chinese A. feae. Read More

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Distribution of Merlin in eukaryotes and first report of DNA transposons in kinetoplastid protists.

PLoS One 2021 6;16(5):e0251133. Epub 2021 May 6.

Laboratório de Ciências e Tecnologias Aplicadas em Saúde (LaCTAS), Instituto Carlos Chagas, Fundação Oswaldo Cruz (Fiocruz), Curitiba, PR, Brazil.

DNA transposons are defined as repeated DNA sequences that can move within the host genome through the action of transposases. The transposon superfamily Merlin was originally found mainly in animal genomes. Here, we describe a global distribution of the Merlin in animals, fungi, plants and protists, reporting for the first time their presence in Rhodophyceae, Metamonada, Discoba and Alveolata. Read More

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Analysis of putative quadruplex-forming sequences in fungal genomes: novel antifungal targets?

Microb Genom 2021 May;7(5)

School of Biological Sciences, University of East Anglia, Norwich, UK.

Fungal infections cause >1 million deaths annually and the emergence of antifungal resistance has prompted the exploration for novel antifungal targets. Quadruplexes are four-stranded nucleic acid secondary structures, which can regulate processes such as transcription, translation, replication and recombination. They are also found in genes linked to virulence in microbes, and ligands that bind to quadruplexes can eliminate drug-resistant pathogens. Read More

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Molecular characterization of a novel single-stranded RNA virus, ChRV1, isolated from the plant-pathogenic fungus Colletotrichum higginsianum.

Arch Virol 2021 May 6. Epub 2021 May 6.

Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Nongda Road 1, Furong District, Changsha, 410128, Hunan, People's Republic of China.

In this study, a novel single-stranded RNA virus was isolated from the plant-pathogenic fungus Colletotrichum higginsianum strain HTC-5, and the virus was named "Colletotrichum higginsianum ssRNA virus 1" (ChRV1). The complete genome of ChRV1 is 3850 nucleotides in length with a GC content of 52% and contains two in-frame open reading frames (ORFs): ORF1 (smaller) and ORF2 (larger). ORF1 encodes a protein with the highest sequence similarity to proteins encoded by Phoma matteucciicola RNA virus 1 (PmRV1, 47. Read More

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Compound heterozygous p. Arg949Trp and p. Gly970Ala mutations deteriorated the function of PEX1p: A study on PEX1 in a patient with Zellweger syndrome.

J Cell Biochem 2021 May 6. Epub 2021 May 6.

Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Postal Code 81746-73441, Iran.

The peroxisome is responsible for a variety of vital pathways in primary metabolism, including the very long-chain fatty-acid oxidation and plasmalogen lipid biosynthesis. Autosomal recessive disorder of the Zellweger spectrum (ZSD) is a major subset of peroxisome biogenesis disorders (PBDs) that can be caused by mutations in any of the 14 PEX genes. Zellweger syndrome (ZS) is the foremost common and severe phenotype within the heterogeneous ZSD. Read More

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