Transcript map of the temperate Lactobacillus gasseri bacteriophage ϕadh

Microbiology ◽  
2003 ◽  
Vol 149 (10) ◽  
pp. 2987-2999 ◽  
Author(s):  
Eric Altermann ◽  
Bernhard Henrich
Keyword(s):  
Replication Origin ◽  
Phage Genome ◽  
Attachment Site ◽  
Genomic Region ◽  
Dna Packaging ◽  
Middle Region ◽  
Late Transcription ◽  
Early Transcription ◽  
Transcript Map ◽  
Overlapping Transcripts

Temporal transcription of phage ϕadh was analysed during lytic reproduction. Based on Northern hybridizations the phage genome was divided into regions of early, middle and late transcription. Eight groups of overlapping transcripts, probably originating from common precursors, were distinguished. Early transcription of a 10·9 kb region adjacent to the lytic/lysogenic switch started within the first 10 min of infection and produced three groups of mRNAs mostly related to DNA replication. Four middle transcripts were observed 30 min after infection, corresponding to an 8·5 kb genomic region, which started at the replication origin (ori) and encompassed a DNA packaging function and the cos site. Three groups of late transcripts were first observed 50 min after infection, corresponding to a 21·1 kb region between the middle region and the attachment site (attP), encoding functions for capsid morphogenesis and host cell lysis. A fourth group of late-appearing mRNAs was divergently transcribed from the 3·2 kb section between attP and the lytic/lysogenic switch, including the repressor and integrase genes. Except for one set of early mRNAs, all the transcripts persisted until the end of the reproduction cycle. Two confirmed and two predicted promoters were assigned to transcript 5′ ends in the early region.

scholarly journals An alternative route of bacterial infection associated with a novel resistance locus in the Daphnia–Pasteuria host–parasite system

Heredity ◽  
2020 ◽  
Vol 125 (4) ◽  
pp. 173-183
Author(s):  
Gilberto Bento ◽  
Peter D. Fields ◽  
David Duneau ◽  
Dieter Ebert
Keyword(s):  
Host Resistance ◽  
Natural Populations ◽  
Attachment Site ◽  
Genomic Region ◽  
Infection Process ◽  
Resistance Locus ◽  
Significant Qtls ◽  
Novel Host ◽  
Trait Locus ◽  
Host Parasite

Abstract To understand the mechanisms of antagonistic coevolution, it is crucial to identify the genetics of parasite resistance. In the Daphnia magna–Pasteuria ramosa host–parasite system, the most important step of the infection process is the one in which P. ramosa spores attach to the host’s foregut. A matching-allele model (MAM) describes the host–parasite genetic interactions underlying attachment success. Here we describe a new P. ramosa genotype, P15, which, unlike previously studied genotypes, attaches to the host’s hindgut, not to its foregut. Host resistance to P15 attachment shows great diversity across natural populations. In contrast to P. ramosa genotypes that use foregut attachment, P15 shows some quantitative variation in attachment success and does not always lead to successful infections, suggesting that hindgut attachment represents a less-efficient infection mechanism than foregut attachment. Using a Quantitative Trait Locus (QTL) approach, we detect two significant QTLs in the host genome: one that co-localizes with the previously described D. magna PR locus of resistance to foregut attachment, and a second, major QTL located in an unlinked genomic region. We find no evidence of epistasis. Fine mapping reveals a genomic region, the D locus, of ~13 kb. The discovery of a second P. ramosa attachment site and of a novel host-resistance locus increases the complexity of this system, with implications for both for the coevolutionary dynamics (e.g., Red Queen and the role of recombination), and for the evolution and epidemiology of the infection process.

scholarly journals Transcriptional Landscape of Staphylococcus aureus Kayvirus Bacteriophage vB_SauM-515A1

Viruses ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 1320
Author(s):  
Maria Kornienko ◽  
Gleb Fisunov ◽  
Dmitry Bespiatykh ◽  
Nikita Kuptsov ◽  
Roman Gorodnichev ◽  
...  
Keyword(s):  
Phage Genome ◽  
Expression Profiles ◽  
Consensus Sequence ◽  
General Interest ◽  
Broad Host Range ◽  
Bacteriophage Therapy ◽  
Late Transcription ◽  
Characteristic Features ◽  
Sigma 70 ◽  
And Control

The Twort-like myoviruses (Kayvirus genus) of S. aureus are promising agents for bacteriophage therapy due to a broad host range and high killing activity against clinical isolates. This work improves the current understanding of the phage infection physiology by transcriptome analysis. The expression profiles of a typical member of the Kayvirus genus (vB_SauM-515A1) were obtained at three time-points post-infection using RNA sequencing. A total of 35 transcription units comprising 238 ORFs were established. The sequences for 58 early and 12 late promoters were identified in the phage genome. The early promoters represent the strong sigma-70 promoters consensus sequence and control the host-dependent expression of 26 transcription units (81% of genes). The late promoters exclusively controlled the expression of four transcription units, while the transcription of the other five units was directed by both types of promoters. The characteristic features of late promoters were long -10 box of TGTTATATTA consensus sequence and the absence of -35 boxes. The data obtained are also of general interest, demonstrating a strategy of the phage genome expression with a broad overlap of the early and late transcription phases without any middle transcription, which is unusual for the large phage genomes (>100 kbp).

Transcript Map of a 900-kb Genomic Region in Xp22.1–p22.2: Identification of 12 Novel Genes

Genomics ◽  
1998 ◽  
Vol 51 (1) ◽  
pp. 59-67 ◽  
Author(s):  
Regina Warneke-Wittstock ◽  
Andreas Marquardt ◽  
Andrea Gehrig ◽  
Christian G. Sauer ◽  
Manfred Gessler ◽  
...  
Keyword(s):  
Genomic Region ◽  
Novel Genes ◽  
Transcript Map

scholarly journals Directed Nucleosome Sliding during the Formation of the Simian Virus 40 Particle Exposes DNA Sequences Required for Early Transcription

2018 ◽  
Vol 93 (4) ◽  
Author(s):  
Meera Ajeet Kumar ◽  
Karine Kasti ◽  
Lata Balakrishnan ◽  
Barry Milavetz
Keyword(s):  
Life Cycle ◽  
Histone Modifications ◽  
Late Stage ◽  
Binding Sites ◽  
Regulatory Region ◽  
Simian Virus 40 ◽  
Simian Virus ◽  
Late Transcription ◽  
Early Transcription

ABSTRACTSimian virus 40 (SV40) exists as chromatin throughout its life cycle and undergoes typical epigenetic regulation mediated by changes in nucleosome location and associated histone modifications. In order to investigate the role of epigenetic regulation during the encapsidation of late-stage minichromosomes into virions, we mapped the locations of nucleosomes containing acetylated or methylated lysines in the histone tails of H3 and H4 present in the chromatin from 48-h-postinfection minichromosomes and disrupted virions. In minichromosomes obtained late in infection, nucleosomes were found carrying various histone modifications primarily in the regulatory region, with a major nucleosome located within the enhancer and other nucleosomes at the early and late transcriptional start sites. The nucleosome found in the enhancer would be expected to repress early transcription by blocking access to part of the SP1 binding sites and the left side of the enhancer in late-stage minichromosomes while also allowing late transcription. In chromatin from virions, the principal nucleosome located in the enhancer was shifted ∼70 bases in the late direction from what was found in minichromosomes, and the level of modified histones was increased throughout the genome. The shifting of the enhancer-associated nucleosome to the late side would effectively serve as a switch to relieve the repression of early transcription found in late minichromosomes while likely also repressing late transcription by blocking access to necessary regulatory sequences. This epigenetic switch appeared to occur during the final stage of virion formation.IMPORTANCEFor a virus to complete infection, it must produce a new virus particle in which the genome is able to support a new infection. This is particularly important for viruses like simian virus 40 (SV40), which exist as chromatin throughout their life cycles, since chromatin structure plays a major role in the regulation of the life cycle. In order to determine the role of SV40 chromatin structure late in infection, we mapped the locations of nucleosomes and their histone tail modifications in SV40 minichromosomes and in the SV40 chromatin found in virions using chromatin immunoprecipitation-DNA sequencing (ChIP-Seq). We have identified a novel viral transcriptional control mechanism in which a nucleosome found in the regulatory region of the SV40 minichromosome is directed to slide during the formation of the virus particle, exposing transcription factor binding sites required for early transcription that were previously blocked by the presence of the nucleosome.

scholarly journals Lactococcal 949 Group Phages Recognize a Carbohydrate Receptor on the Host Cell Surface

2015 ◽  
Vol 81 (10) ◽  
pp. 3299-3305 ◽  
Author(s):  
Jennifer Mahony ◽  
Walter Randazzo ◽  
Horst Neve ◽  
Luca Settanni ◽  
Douwe van Sinderen
Keyword(s):  
Cheese Whey ◽  
Phage Genome ◽  
Bioinformatic Analysis ◽  
Genomic Region ◽  
Open Reading Frames ◽  
Host Recognition ◽  
Phage Group ◽  
Host Cell Surface ◽  
Reading Frames ◽  
Dairy Fermentation

ABSTRACTLactococcal bacteriophages represent one of the leading causes of dairy fermentation failure and product inconsistencies. A new member of the lactococcal 949 phage group, named WRP3, was isolated from cheese whey from a Sicilian factory in 2011. The genome sequence of this phage was determined, and it constitutes the largest lactococcal phage genome currently known, at 130,008 bp. Detailed bioinformatic analysis of the genomic region encoding the presumed initiator complex and baseplate of WRP3 has aided in the functional assignment of several open reading frames (ORFs), particularly that for the receptor binding protein required for host recognition. Furthermore, we demonstrate that the 949 phages target cell wall phospho-polysaccharides as their receptors, accounting for the specificity of the interactions of these phages with their lactococcal hosts. Such information may ultimately aid in the identification of strains/strain blends that do not present the necessary saccharidic target for infection by these problematic phages.

scholarly journals The BSGatlas: An enhanced annotation of genes and transcripts for the Bacillus subtilis genome with improved information access

2019 ◽  
Author(s):  
Adrian Sven Geissler ◽  
Christian Anthon ◽  
Enrique González-Tortuero ◽  
Line Dahl Poulsen ◽  
Thomas Beuchert Kallehauge ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
High Throughput ◽  
Large Scale ◽  
Information Access ◽  
Fold Increase ◽  
Genomic Region ◽  
Transcription Start Sites ◽  
Genomic Knowledge ◽  
The Individual ◽  
Transcript Map

AbstractThe genome of Bacillus subtilis continues to provide exiting genomic insights. However, the growing collective genomic knowledge about this micro-organism is spread across multiple annotation resources. Thus, the full annotation is not directly accessible neither for specific genes nor for large-scale high-throughput analyses. Furthermore, access to annotation of non-coding RNA genes (ncRNAs) and polycistronic mRNAs is difficult. To address these challenges we introduce the Bacillus subtilis genome atlas, BSGatlas, in which we integrate and unify multiple existing annotation resources. Our integration provides twice as many ncRNAs than the individual resources, improves the positional annotation for 70% of the combined ncRNAs, and makes it possible to infer specific ncRNA types. Moreover, we unify known transcription start sites, termination, and transcriptional units (TUs) as a comprehensive transcript map. This transcript map implies 815 new TUs and 6, 164 untranslated regions (UTRs), which is a five-fold increase over existing resources. We furthermore, find 2, 309 operons covering the transcriptional annotation for 93% of all genes, corresponding to an improvement by 11%. The BSGatlas is available in multiple formats. A user can either download the entire annotation in the standardized GFF3 format, which is compatible with most bioinformatics tools for omics and high-throughput studies, or view the annotation in an online browser at http://rth.dk/resources/bsgatlas.ImportanceThe Bacillus subtilis genome has been studied in numerous context and consequently multiple efforts have been made in providing a complete annotation. Unfortunately, a number of resources are no longer maintained, and (i) the collective annotation knowledge is dispersed over multiple resources, of which each has a different focus of what type of annotation information they provide. (ii) Thus, it is difficult to easily and at a large scale obtain information for a genomic region or genes of interest. (iii) Furthermore, all resources are essentially incomplete when it comes to annotating non-coding and structured RNA, and transcripts in general. Here, we address all three problems by first collecting existing annotations of genes and transcripts start and termination sites; afterwards resolving discrepancies in annotations and combining them, which doubled the number of ncRNAs; inferring full transcripts and 2,309 operons from the combined knowledge of known transcript boundaries and meta-information; and critically providing it all in a standardized UCSC browser. That interface and its powerful set of functionalities allow users to access all the information in a single resource as well as enables them to include own data on top the full annotation.

Germline Transformation Using a prune cDNA Rescues prune/Killer of prune Lethality and the prune Eye Color Phenotype in Drosophila

Genetics ◽  
1996 ◽  
Vol 144 (4) ◽  
pp. 1589-1600 ◽  
Author(s):  
Lisa Timmons ◽  
Allen Shearn
Keyword(s):  
Dna Sequences ◽  
Mutant Gene ◽  
Transcription Unit ◽  
Genomic Region ◽  
Convincing Evidence ◽  
Mutant Proteins ◽  
Eye Color ◽  
Pigment Accumulation ◽  
Overlapping Transcripts ◽  
Color Phenotype

Null mutations in the prune gene of Drosophila melanogaster result in prune eye color due to reductions in red pigment accumulation. When one copy of the awdKiller of prune mutant gene is present in a prune background, the animals die. The cause of prune/Killer of prune lethality remains unknown. The genomic region characterized for the prune locus is transcriptionally active and complex, with multiple and overlapping transcripts. Despite the transcriptional complexity of the genomic region of prune, accumulated evidence suggests that the prune locus is small and consists of a single transcription unit, since every prune allele to date exhibits both prune eye color and prune/Killer of prune lethality. A functional prune product from a single, full-length cDNA was identified in this study that can rescue both the eye phenotype and prune/Killer of prune lethality. The DNA sequences of several mutant prune alleles along with Western blot analysis of mutant proteins provide convincing evidence that prune mutations are nulls, and that the cDNA identified in this study encodes the only product of the prune locus.

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