183,078 results match your criteria promoter sequence

Characterization of DinJ-YafQ toxin-antitoxin module in Tetragenococcus halophilus: activity, interplay, and evolution.

Appl Microbiol Biotechnol 2021 Apr 20. Epub 2021 Apr 20.

School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China.

Tetragenococcus halophilus is a moderately halophilic lactic acid bacterium widely used in high-salt food fermentation because of its coping ability under various stress conditions. Bacterial toxin-antitoxin (TA) modules are widely distributed and play important roles in stress response, but those specific for genus Tetragenococcus have never been explored. Here, a bona fide TA module named DinJ-YafQ was characterized in T. Read More

View Article and Full-Text PDF

Sequencing of a Wild Apple (Malus baccata) Genome Unravels the Differences Between Cultivated and Wild Apple Species Regarding Disease Resistance and Cold Tolerance.

G3 (Bethesda) 2019 Jul;9(7):2051-2060

College of Life Sciences, Northwest A&F University, Yangling 712100, Shannxi, China.

Malus baccata is one of four wild apple species that can hybridize with the cultivated apple species (Malus domestica). It is widely used in high-latitude apple-producing areas as a rootstock and breeding resource because of its disease resistance, and cold tolerance. A lack of a reference genome has limited the application of M. Read More

View Article and Full-Text PDF

Functional Study of the Type II-A CRISPR-Cas System of Hypervirulent Strains.

CRISPR J 2021 Apr;4(2):233-242

ISP, Université de Tours, INRAE, Tours, France; Dangé-Saint-Romain, France.

Nearly all strains of , the leading cause of invasive infections in neonates, encode a type II-A clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system. Interestingly, strains belonging to the hypervirulent Sequence Type 17 (ST17) contain significantly fewer spacers in their CRISPR locus than other lineages, which could be the result of a less functional CRISPR-Cas system. Here, we revealed one large deletion in the ST17 promoter region and we evaluated its impact on the transcription of genes as well as the functionalities of the CRISPR-Cas system. Read More

View Article and Full-Text PDF

Nisin variants from Streptococcus and Staphylococcus successfully express in Lactococcus lactis NZ9800.

J Appl Microbiol 2021 Apr 19. Epub 2021 Apr 19.

Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland.

Aims: Increases in antimicrobial resistance has meant that the antimicrobial potential of lantibiotics is now being investigated irrespective of the nature of the producing organism. The aim of this study was to investigate if natural nisin variants produced by non- GRAS strains, such as nisin H, nisin J and nisin P, could be expressed in a well characterized GRAS host.

Methods And Results: This study involved cloning the nisin A promoter and leader sequence fused to either nisin H, nisin J or nisin P structural gene sequences originally produced by Streptococcus hyointestinalis DPC 6484, Staphylococcus capitis APC 2923, and Streptococcus agalactiae DPC 7040, respectively. Read More

View Article and Full-Text PDF

Biochemistry and molecular biology of lignification.

New Phytol 1995 Feb;129(2):203-236

Centre de Biologic et Physiologic Végétales, URA CNRS 1941, Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse Cedex, France.

Lignins, which result from the dehydrogenative polymerization of cinnamyl alcohols, are complex heteropolymers deposited in the walls of specific cells of higher plants. Lignins have probably been associated to land colonization by plants but several aspects concerning their biosynthesis, structure and function are still only partially understood. This review focuses on the modern physicochemical methods of structural analysis of lignins, and on the new approaches of molecular biology and genetic engineering applied to lignification. Read More

View Article and Full-Text PDF
February 1995

Whole genome deep sequencing analysis of viral quasispecies diversity and evolution in HBeAg seroconverters.

JHEP Rep 2021 Jun 18;3(3):100254. Epub 2021 Feb 18.

Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan.

Background & Aims: We aimed to investigate how viral quasispecies of the HBV whole genome evolves and diversifies in response to HBeAg seroconversion and viral control utilising next-generation sequencing (NGS).

Methods: Fifty HBeAg-positive chronic hepatitis B patients, including 18 treatment-naïve and 32 interferon (IFN)-treated individuals, were recruited. Serial HBV whole genomes in serum were analysed by NGS to determine sequence characteristics and viral quasispecies. Read More

View Article and Full-Text PDF

Antiviral Activity of Interferon Alpha-Inducible Protein 27 Against Hepatitis B Virus Gene Expression and Replication.

Front Microbiol 2021 31;12:656353. Epub 2021 Mar 31.

State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China.

Despite the availability of effective vaccines, hepatitis B virus (HBV) is still a major health issue, and approximately 350 million people have been chronically infected with HBV throughout the world. Interferons (IFNs) are the key molecules in the innate immune response that restrict several kinds of viral infections the induction of hundreds of IFN-stimulated genes (ISGs). The objective of this study was to confirm if interferon alpha-inducible protein 27 (IFI27) as an ISG could inhibit HBV gene expression and DNA replication both in cell culture and in a mouse model. Read More

View Article and Full-Text PDF

Genomic Diversity and Virulence Potential of ESBL- and AmpC-β-Lactamase-Producing Strains From Healthy Food Animals Across Europe.

Front Microbiol 2021 1;12:626774. Epub 2021 Apr 1.

NG1 Microbial Genomics, Robert Koch Institute, Berlin, Germany.

The role of livestock animals as a putative source of ESBL/pAmpC for humans is a central issue of research. In a large-scale pan-European surveillance, 2,993 commensal spp. isolates were recovered from randomly collected fecal samples of healthy cattle, pigs and chickens in various abattoirs. Read More

View Article and Full-Text PDF

A key 'foxy' aroma gene is regulated by homology-induced promoter indels in the iconic juice grape 'Concord'.

Hortic Res 2020 Apr 18;7(1):67. Epub 2020 Apr 18.

US Department of Agriculture-Agricultural Research Service, Grape Genetics Research Unit, Geneva, NY, USA.

'Concord', the most well-known juice grape with a parentage of the North American grape species Vitis labrusca L., possesses a special 'foxy' aroma predominantly resulted from the accumulation of methyl anthranilate (MA) in berries. This aroma, however, is often perceived as an undesirable attribute by wine consumers and rarely noticeable in the common table and wine grape species V. Read More

View Article and Full-Text PDF

Functional analysis and expression patterns of members of the FLOWERING LOCUS T (FT) gene family in Lilium.

Plant Physiol Biochem 2021 Apr 5;163:250-260. Epub 2021 Apr 5.

Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China. Electronic address:

Lilium is an important commercial flowering species, and there are many varieties and more than 100 species of wild Lilium. Lilium × formolongi is usually propagated from seedlings, and the flowering of these plants is driven mainly by the photoperiodic pathway. Most of the other lily plants are propagated via bulblets and need to be vernalized; these plants can be simply divided into pretransplantation types and posttransplantation types according to the time at which the floral transition occurs. Read More

View Article and Full-Text PDF

Generation of human induced pluripotent stem cell lines (UNIMGi003-A and UNIMGi004-A) from two Italian siblings affected by Unverricht-Lundborg disease.

Stem Cell Res 2021 Apr 9;53:102329. Epub 2021 Apr 9.

Department of Clinical and Experimental Medicine, Magna Græcia University, 88100 Catanzaro, Italy. Electronic address:

Unverricht-Lundborg disease (ULD) is an inherited form of progressive myoclonus epilepsy caused by mutations in the gene encoding Cystatin B (CSTB), an inhibitor of lysosomal proteases. The most common mutation described in ULD patients is an unstable expansion of a dodecamer sequence located in the CSTB gene promoter. This expansion is causative of the downregulation of CSTB gene expression and, consequently, of its inhibitory activity. Read More

View Article and Full-Text PDF

A transcriptional regulatory module controls lipid accumulation in soybean.

New Phytol 2021 Apr 17. Epub 2021 Apr 17.

State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, 100101, China.

Soybean (Glycine max) is one of the most important oilseed crops. However, limited information is known about the regulatory mechanism of oil accumulation in soybean. In this study, a member of tandem CCCH zinc finger (TZF) proteins, GmZF392, from our previous RNA-seq analysis for seed-preferred transcription factors, was found to function as a positive regulator of lipid production. Read More

View Article and Full-Text PDF

Improving the design of an oxidative stress sensing biosensor in yeast.

FEMS Yeast Res 2021 Apr 17. Epub 2021 Apr 17.

Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, M5S 1A1, Canada.

Transcription factor (TF)-based biosensors have proven useful for increasing biomanufacturing yields, large-scale functional screening, and in environmental monitoring. Most yeast TF-based biosensors are built from natural promoters, resulting in large DNA parts retaining considerable homology to the host genome, which can complicate biological engineering efforts. There is a need to explore smaller, synthetic biosensors to expand the options for regulating gene expression in yeast. Read More

View Article and Full-Text PDF

Deletion of CTCF sites in the SHH locus alters enhancer-promoter interactions and leads to acheiropodia.

Nat Commun 2021 04 16;12(1):2282. Epub 2021 Apr 16.

Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.

Acheiropodia, congenital limb truncation, is associated with homozygous deletions in the LMBR1 gene around ZRS, an enhancer regulating SHH during limb development. How these deletions lead to this phenotype is unknown. Using whole-genome sequencing, we fine-mapped the acheiropodia-associated region to 12 kb and show that it does not function as an enhancer. Read More

View Article and Full-Text PDF

Nuclear ErbB2 represses DEPTOR transcription to inhibit autophagy in breast cancer cells.

Cell Death Dis 2021 Apr 14;12(4):397. Epub 2021 Apr 14.

Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.

ErbB2, a classical receptor tyrosine kinase, is frequently overexpressed in breast cancer cells. Although the role of ErbB2 in the transmission of extracellular signals to intracellular matrix has been widely studied, the functions of nuclear ErbB2 remain largely elusive. Here, we report a novel function of nuclear ErbB2 in repressing the transcription of DEPTOR, a direct inhibitor of mTOR. Read More

View Article and Full-Text PDF

Nicotinamide adenine dinucleotide phosphate (NADPH) oxidase p22phox subunit polymorphisms, systemic oxidative stress, endothelial dysfunction, and atherosclerosis in type 2 diabetes mellitus.

Pol Arch Intern Med 2021 Apr 14. Epub 2021 Apr 14.

Introduction: Diabetes mellitus is an important and rapidly increasing problem in public health. It associates with endothelial dysfunction and increased endothelial permeability, which may lead to severe cardiovascular events.

Objectives: We aimed to evaluate the relationship between polymorphisms in the cytochrome b-245 alpha chain (CYBA) gene encoding p22phox, a key subunit of nicotinamide adenine dinucleotide phosphate (NADPH) oxidase, with endothelial function, atherosclerosis and systemic oxidative stress in type 2 diabetes mellitus (T2DM). Read More

View Article and Full-Text PDF

Development of a Novel Human CD147 Transgenic NSG Mouse Model to test SARS-CoV-2 Infection and Immune Responses.

Res Sq 2021 Apr 7. Epub 2021 Apr 7.

An animal model that can mimic the SARS-CoV-2 infection in humans is critical to understanding the newly emerged, rapidly spreading SARS-CoV-2 and development of therapeutic strategies. Studies show that the spike (S) proteins of SARS-CoV (SARS-CoV-S-1-S) and SARS-CoV-2 (SARS-CoV-2-S) bind to human angiotensin-converting enzyme 2 (hACE2, a well-recognized, functional receptor for SARS-CoV and SARS-CoV-2) to mediate viral entry. Several hACE2 transgenic (hACE2Tg) mouse models are being widely used, which is clearly invaluable. Read More

View Article and Full-Text PDF

Length variation in short tandem repeats affects gene expression in natural populations of Arabidopsis thaliana.

Plant Cell 2021 Apr 12. Epub 2021 Apr 12.

Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, 0316 Oslo, Norway.

The genetic basis for the fine-tuned regulation of gene expression is complex and ultimately influences the phenotype and thus the local adaptation of natural populations. Short tandem repeats (STRs) consisting of repetitive DNA motifs have been shown to regulate gene expression. STRs are variable in length within a population and serve as a heritable, but semi-reversible, reservoir of standing genetic variation. Read More

View Article and Full-Text PDF

Identification and functional characterization of two bamboo FD gene homologs having contrasting effects on shoot growth and flowering.

Sci Rep 2021 Apr 12;11(1):7849. Epub 2021 Apr 12.

Department of Life Sciences, Presidency University, Kolkata, India.

Bamboos, member of the family Poaceae, represent many interesting features with respect to their fast and extended vegetative growth, unusual, yet divergent flowering time across species, and impact of sudden, large scale flowering on forest ecology. However, not many studies have been conducted at the molecular level to characterize important genes that regulate vegetative and flowering habit in bamboo. In this study, two bamboo FD genes, BtFD1 and BtFD2, which are members of the florigen activation complex (FAC) have been identified by sequence and phylogenetic analyses. Read More

View Article and Full-Text PDF

An efficient vector-based CRISPR/Cas9 system in an Oreochromis mossambicus cell line using endogenous promoters.

Sci Rep 2021 Apr 12;11(1):7854. Epub 2021 Apr 12.

Biochemical Evolution Laboratory, Department of Animal Science, University of California, Davis, CA, 95616, USA.

CRISPR/Cas9 gene editing is effective in manipulating genetic loci in mammalian cell cultures and whole fish but efficient platforms applicable to fish cell lines are currently limited. Our initial attempts to employ this technology in fish cell lines using heterologous promoters or a ribonucleoprotein approach failed to indicate genomic alteration at targeted sites in a tilapia brain cell line (OmB). For potential use in a DNA vector approach, endogenous tilapia beta Actin (OmBAct), EF1 alpha (OmEF1a), and U6 (TU6) promoters were isolated. Read More

View Article and Full-Text PDF

A trigger phosphodiesterase modulates the global c-di-GMP pool, motility and biofilm formation in .

J Bacteriol 2021 Apr 12. Epub 2021 Apr 12.

Programa de Biología de Sistemas y Biología Sintética, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México.

cells transit from free swimming to surface adapted lifestyles, such as swarming colonies and three-dimensional biofilms. These transitions are regulated by sensory modules and regulatory networks that involve the second messenger cyclic dimeric guanosine monophosphate (c-di-GMP). In this work, we show that a previously uncharacterized c-di-GMP phosphodiesterase (VP1881) from plays an important role in modulating the c-di-GMP pool. Read More

View Article and Full-Text PDF

Development of multiplexing gene silencing system using conditionally induced polycistronic synthetic antisense RNAs in Escherichia coli.

Biochem Biophys Res Commun 2021 Apr 9;556:163-170. Epub 2021 Apr 9.

Department of Human Nutrition, Faculty of Contemporary Life Science, Chugokugakuen University, Okayama, Japan. Electronic address:

Although efficient methods of gene silencing have been established in eukaryotes, many different techniques are still used in bacteria due to the lack of a standardized tool. Here, we developed a convenient and efficient method to downregulate the expression of a specific gene using ∼140 nucleotide RNA with a 24-nucleotide antisense region from an arabinose-inducible expression plasmid by taking Escherichia coli lacZ and phoA genes encoding β-galactosidase and alkaline phosphatase, respectively, as target genes to evaluate the model. We examined the antisense RNA (asRNA) design, including targeting position, uORF stability elements at the 5'-end, and Hfq-binding module at the 3'-end, and inducer amount required to obtain effective experimental conditions for gene silencing. Read More

View Article and Full-Text PDF

LASS2 mediates Nrf2-driven progestin resistance in endometrial cancer.

Am J Transl Res 2021 15;13(3):1280-1289. Epub 2021 Mar 15.

Jiangxi Medical College, Nanchang University Nanchang 330000, China.

Progestin administration serves as the optimal conservative treatment method for women with endometrial cancer or precancer lesions who want to preserve fertility. However, there are still at least 30% of patients in which progestin resistance occurs. LASS2 (Ceramide Synthase 2) has been reported to be involved in chemotherapy resistance, whether it also plays a role in progestin resistance is not clear. Read More

View Article and Full-Text PDF

Induction of resistance to sugarcane mosaic virus by RNA interference targeting coat protein gene silencing in transgenic sugarcane.

Mol Biol Rep 2021 Apr 10. Epub 2021 Apr 10.

Laboratory of Molecular Biology and Biotechnology, Center for Development of Advanced Science and Technology (CDAST), Jember University, Jln. Kalimantan 37, Jember, 68121, Indonesia.

Sugarcane mosaic virus (SCMV) is a serious disease of monocotyledonous plants, including sugarcane, causing deterioration in both growth and productivity. RNA interference (RNAi) inhibits gene expression through RNA-mediated sequence-specific interactions and is considered an effective approach to control viral infection in plants. In this study, the SCMVCp gene encoding the coat protein (CP) was inserted into the pGreen-0179 plasmid in both sense and antisense orientations. Read More

View Article and Full-Text PDF

Pituitary tumors and immortalized cell lines generated by cre-inducible expression of SV40 T antigen.

Endocrinology 2021 Apr 10. Epub 2021 Apr 10.

University of Michigan Medical School, Ann Arbor, MI, USA.

Targeted oncogenesis is the process of driving tumor formation by engineering transgenic mice that express an oncogene under the control of a cell-type specific promoter. Such tumors can be adapted to cell culture, providing immortalized cell lines. To make it feasible to follow the process of tumorigenesis and increase the opportunity for generating cell lines, we developed a mouse strain that expresses SV40 T antigens in response to cre-recombinase. Read More

View Article and Full-Text PDF

Interpretation of allele-specific chromatin accessibility using cell state-aware deep learning.

Genome Res 2021 Apr 8. Epub 2021 Apr 8.

VIB-KU Leuven Center for Brain & Disease Research, KU Leuven;

Genomic sequence variation within enhancers and promoters can have a significant impact on the cellular state and phenotype. However, sifting through the millions of candidate variants in a personal genome or a cancer genome, to identify those that impact -regulatory function, remains a major challenge. Interpretation of noncoding genome variation benefits from explainable artificial intelligence to predict and interpret the impact of a mutation on gene regulation. Read More

View Article and Full-Text PDF

[A homozygous variant in a consanguineous pedigree with inherited protein S deficiency].

Zhonghua Jie He He Hu Xi Za Zhi 2021 Apr;44(4):360-364

Center of Laboratory Medicine, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325015, China.

To observe the clinical feature of familiar hereditary protein S deficiency, and to explore the related gene mutation. The blood samples were obtained from the proband and the family memebers(3 generations,6 persons). gene of the proband and the family members was analyzed. Read More

View Article and Full-Text PDF

Natural variation in APX9 is associated with a yield-enhancing QTL cluster in rice.

J Exp Bot 2021 Apr 8. Epub 2021 Apr 8.

Department of Agronomy, College of Agricultural and Life Science, Chungnam National University, Daejeon, Republic of Korea.

We previously identified a cluster of yield-related QTL including plant height and heading date in CR4379, a near-isogenic line from an interspecific cross between Oryza sativa spp. japonica cultivar 'Hwaseong' and the wild relative O. rufipogon. Read More

View Article and Full-Text PDF

Plasmid-Chromosome Crosstalk in : A Horizontally Acquired Transcription Regulator Controls Polysaccharide Intercellular Adhesin-Mediated Biofilm Formation.

Front Cell Infect Microbiol 2021 22;11:660702. Epub 2021 Mar 22.

Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany.

Livestock-associated methicillin-resistant (LA-MRSA) of clonal complex CC398 typically carry various antimicrobial resistance genes, many of them located on plasmids. In the bovine LA-MRSA isolate Rd11, we previously identified plasmid pAFS11 in which resistance genes are co-localized with a novel -like gene cluster, harboring genes required for polysaccharide intercellular adhesin (PIA)-mediated biofilm formation. The genes on pAFS11 were acquired in addition to a pre-existing locus on the  Rd11 chromosomal DNA. Read More

View Article and Full-Text PDF

Epigenetic reprogramming of tumor cell-intrinsic STING function sculpts antigenicity and T cell recognition of melanoma.

Proc Natl Acad Sci U S A 2021 Apr;118(15)

Department of Immunology, Moffitt Cancer Center, Tampa, FL 33612;

Lack or loss of tumor antigenicity represents one of the key mechanisms of immune escape and resistance to T cell-based immunotherapies. Evidence suggests that activation of stimulator of interferon genes (STING) signaling in tumor cells can augment their antigenicity by triggering a type I IFN-mediated sequence of autocrine and paracrine events. Although suppression of this pathway in melanoma and other tumor types has been consistently reported, the mechanistic basis remains unclear. Read More

View Article and Full-Text PDF