scholarly journals Temporal Global Changes in Gene Expression during Temperature Transition in Yersinia pestis

2004 ◽  
Vol 186 (18) ◽  
pp. 6298-6305 ◽  
Author(s):  
Vladimir L. Motin ◽  
Anca M. Georgescu ◽  
Joseph P. Fitch ◽  
Pauline P. Gu ◽  
David O. Nelson ◽  
...  
Keyword(s):  
Yersinia Pestis ◽  
Dna Microarrays ◽  
Open Reading Frames ◽  
Mammalian Host ◽  
Global Changes ◽  
Temperature Transition ◽  
Entire Genome ◽  
Regulatory Changes ◽  
Chromosomal Genes ◽  
Reading Frames

ABSTRACT DNA microarrays encompassing the entire genome of Yersinia pestis were used to characterize global regulatory changes during steady-state vegetative growth occurring after shift from 26 to 37°C in the presence and absence of Ca2+. Transcriptional profiles revealed that 51, 4, and 13 respective genes and open reading frames (ORFs) on pCD, pPCP, and pMT were thermoinduced and that the majority of these genes carried by pCD were downregulated by Ca2+. In contrast, Ca2+ had little effect on chromosomal genes and ORFs, of which 235 were thermally upregulated and 274 were thermally downregulated. The primary consequence of these regulatory events is profligate catabolism of numerous metabolites available in the mammalian host.

scholarly journals Genomewide Overexpression Screen for Fosfomycin Resistance in Escherichia coli: MurA Confers Clinical Resistance at Low Fitness Cost

2012 ◽  
Vol 56 (5) ◽  
pp. 2767-2769 ◽  
Author(s):  
Alejandro Couce ◽  
Alejandra Briales ◽  
Alexandro Rodríguez-Rojas ◽  
Coloma Costas ◽  
Álvaro Pascual ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Fitness Cost ◽  
Open Reading Frames ◽  
Content Type ◽  
Clinical Level ◽  
Clinical Resistance ◽  
Chromosomal Genes ◽  
Complete Set ◽  
Fosfomycin Resistance ◽  
Reading Frames

ABSTRACTTo determine whether the overexpression of chromosomal genes can confer fosfomycin resistance, genomewide screening of a complete set of 5,272 plasmid-expressed open reading frames ofEscherichia coli(ASKA collection) was performed. Major results are that (i) no clinical level of resistance is achieved by overexpressing chromosomal genes, exceptmurA; (ii) this level is reached at a low fitness cost; and (iii) this cost is much lower than that imposed by other mutations conferring fosfomycin resistance.

scholarly journals Glycosylation Defects and Virulence Phenotypes ofLeishmania mexicana Phosphomannomutase and Dolicholphosphate-Mannose Synthase Gene Deletion Mutants

2001 ◽  
Vol 21 (23) ◽  
pp. 8168-8183 ◽  
Author(s):  
Attila Garami ◽  
Angela Mehlert ◽  
Thomas Ilg
Keyword(s):  
Gene Deletion ◽  
Open Reading Frames ◽  
Mammalian Host ◽  
Deletion Mutants ◽  
Leishmania Mexicana ◽  
Gpi Anchor ◽  
Gene Encoding ◽  
Mouse Macrophages ◽  
Ample Supply ◽  
Reading Frames

ABSTRACT Leishmania parasites synthesize an abundance of mannose (Man)-containing glycoconjugates thought to be essential for virulence to the mammalian host and for viability. These glycoconjugates include lipophosphoglycan (LPG), proteophosphoglycans (PPGs), glycosylphosphatidylinositol (GPI)-anchored proteins, glycoinositolphospholipids (GIPLs), and N-glycans. A prerequisite for their biosynthesis is an ample supply of the Man donors GDP-Man and dolicholphosphate-Man. We have cloned from Leishmania mexicana the gene encoding the enzyme phosphomannomutase (PMM) and the previously described dolicholphosphate-Man synthase gene (DPMS) that are involved in Man activation. Surprisingly, gene deletion experiments resulted in viable parasite lines lacking the respective open reading frames (ΔPMM and ΔDPMS), a result against expectation and in contrast to the lethal phenotype observed in gene deletion experiments with fungi. L. mexicanaΔDPMS exhibits a selective defect in LPG, protein GPI anchor, and GIPL biosynthesis, but despite the absence of these structures, which have been implicated in parasite virulence and viability, the mutant remains infectious to macrophages and mice. By contrast, L. mexicana ΔPMM are largely devoid of all known Man-containing glycoconjugates and are unable to establish an infection in mouse macrophages or the living animal. Our results define Man activation leading to GDP-Man as a virulence pathway in Leishmania.

scholarly journals Molecular Characterization of IS1541Insertions in the Genome of Yersinia pestis

1998 ◽  
Vol 180 (1) ◽  
pp. 178-181 ◽  
Author(s):  
Monique Odaert ◽  
Annie Devalckenaere ◽  
Patrick Trieu-Cuot ◽  
Michel Simonet
Keyword(s):  
Yersinia Pestis ◽  
Hot Spots ◽  
Insertion Sequence ◽  
Single Copy ◽  
Open Reading Frames ◽  
Stem Loop ◽  
Insertion Sites ◽  
Flanking Regions ◽  
Reading Frames

ABSTRACT The genome of Yersinia pestis, the causative agent of plague, contains at least 30 copies of an element, designated IS1541, which is structurally related to IS200(85% identity). One such element is inserted within the chromosomalinv gene (M. Simonet, B. Riot, N. Fortineau, and P. Berche, Infect. Immun. 64:375–379, 1996). We characterized other IS1541 insertions by cloning 14 different Y. pestis 6/69M loci carrying a single copy of this insertion sequence (IS) into Escherichia coli and, for each element, sequencing 250 bp of both flanking regions. In no case was this IS element inserted into large open reading frames; however, in eight cases, it was detected downstream (17 to 139 bp) of genes thought to be transcribed monocistronically or which constituted the last gene of an operon, and in only one case was it detected upstream (37 bp) of the first gene of an operon. Sequence analysis revealed stem-loop structures (ΔG, <−10 kcal) resembling rho-independent transcription terminators in 8 of the 14 insertion sites. These motifs might constitute hot spots for insertion of this IS1541element within the Y. pestis genome.

scholarly journals DNA Sequencing and Analysis of the Low-Ca2+-Response Plasmid pCD1 of Yersinia pestis KIM5

1998 ◽  
Vol 66 (10) ◽  
pp. 4611-4623 ◽  
Author(s):  
Robert D. Perry ◽  
Susan C. Straley ◽  
Jacqueline D. Fetherston ◽  
Debra J. Rose ◽  
Jason Gregor ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Yersinia Pestis ◽  
Yersinia Pseudotuberculosis ◽  
Gc Content ◽  
Effector Proteins ◽  
Open Reading Frames ◽  
Is Elements ◽  
Virulence Property ◽  
Leucine Rich Repeats ◽  
Reading Frames

ABSTRACT The low-Ca2+-response (LCR) plasmid pCD1 of the plague agent Yersinia pestis KIM5 was sequenced and analyzed for its genetic structure. pCD1 (70,509 bp) has an IncFIIA-like replicon and a SopABC-like partition region. We have assigned 60 apparently intact open reading frames (ORFs) that are not contained within transposable elements. Of these, 47 are proven or possible members of the LCR, a major virulence property of human-pathogenicYersinia spp., that had been identified previously in one or more of Y. pestis or the enteropathogenic yersiniaeYersinia enterocolitica and Yersinia pseudotuberculosis. Of these 47 LCR-related ORFs, 35 constitute a continuous LCR cluster. The other LCR-related ORFs are interspersed among three intact insertion sequence (IS) elements (IS100and two new IS elements, IS1616 and IS1617) and numerous defective or partial transposable elements. Regional variations in percent GC content and among ORFs encoding effector proteins of the LCR are additional evidence of a complex history for this plasmid. Our analysis suggested the possible addition of a new Syc- and Yop-encoding operon to the LCR-related pCD1 genes and gave no support for the existence of YopL. YadA likely is not expressed, as was the case for Y. pestis EV76, and the gene for the lipoprotein YlpA found in Y. enterocolitica likely is a pseudogene in Y. pestis. The yopM gene is longer than previously thought (by a sequence encoding two leucine-rich repeats), the ORF upstream of ypkA-yopJ is discussed as a potential Syc gene, and a previously undescribed ORF downstream ofyopE was identified as being potentially significant. Eight other ORFs not associated with IS elements were identified and deserve future investigation into their functions.

scholarly journals Differential Expression of over 60 Chromosomal Genes in Escherichia coli by Constitutive Expression of MarA

2000 ◽  
Vol 182 (12) ◽  
pp. 3467-3474 ◽  
Author(s):  
Teresa M. Barbosa ◽  
Stuart B. Levy
Keyword(s):  
Escherichia Coli ◽  
Northern Blot Analysis ◽  
Constitutive Expression ◽  
Complete Characterization ◽  
Open Reading Frames ◽  
Altered Expression ◽  
E Coli ◽  
Chromosomal Genes ◽  
Reading Frames

ABSTRACT In Escherichia coli, the MarA protein controls expression of multiple chromosomal genes affecting resistance to antibiotics and other environmental hazards. For a more-complete characterization of the mar regulon, duplicate macroarrays containing 4,290 open reading frames of the E. coli genome were hybridized to radiolabeled cDNA populations derived frommar-deleted and mar-expressing E. coli. Strains constitutively expressing MarA showed altered expression of more than 60 chromosomal genes: 76% showed increased expression and 24% showed decreased expression. Although some of the genes were already known to be MarA regulated, the majority were newly determined and belonged to a variety of functional groups. Some of the genes identified have been associated with iron transport and metabolism; other genes were previously known to be part of thesoxRS regulon. Northern blot analysis of selected genes confirmed the results obtained with the macroarrays. The findings reveal that the mar locus mediates a global stress response involving one of the largest networks of genes described.

scholarly journals yadBC of Yersinia pestis, a New Virulence Determinant for Bubonic Plague

2007 ◽  
Vol 76 (2) ◽  
pp. 578-587 ◽  
Author(s):  
Stanislav Forman ◽  
Christine R. Wulff ◽  
Tanya Myers-Morales ◽  
Clarissa Cowan ◽  
Robert D. Perry ◽  
...  
Keyword(s):  
Epithelial Cells ◽  
Yersinia Pestis ◽  
Potential Surface ◽  
Signal Sequence ◽  
Surface Proteins ◽  
Open Reading Frames ◽  
Large Decrease ◽  
Bubonic Plague ◽  
Epithelioid Cells ◽  
Reading Frames

ABSTRACT In all Yersinia pestis strains examined, the adhesin/invasin yadA gene is a pseudogene, yet Y. pestis is invasive for epithelial cells. To identify potential surface proteins that are structurally and functionally similar to YadA, we searched the Y. pestis genome for open reading frames with homology to yadA and found three: the bicistronic operon yadBC (YPO1387 and YPO1388 of Y. pestis CO92; y2786 and y2785 of Y. pestis KIM5), which encodes two putative surface proteins, and YPO0902, which lacks a signal sequence and likely is nonfunctional. In this study we characterized yadBC regulation and tested the importance of this operon for Y. pestis adherence, invasion, and virulence. We found that loss of yadBC caused a modest loss of invasiveness for epithelioid cells and a large decrease in virulence for bubonic plague but not for pneumonic plague in mice.

scholarly journals Structural Organization of the pFra Virulence-Associated Plasmid of Rhamnose-Positive Yersinia pestis

2004 ◽  
Vol 72 (10) ◽  
pp. 5613-5621 ◽  
Author(s):  
Andrey Golubov ◽  
Heinrich Neubauer ◽  
Christina Nölting ◽  
Jürgen Heesemann ◽  
Alexander Rakin
Keyword(s):  
Yersinia Pestis ◽  
Phospholipase D ◽  
Inner Mongolia ◽  
Structural Organization ◽  
Open Reading Frames ◽  
Geographical Isolation ◽  
Republic Of China ◽  
Transfer Genes ◽  
Conserved Genes ◽  
Reading Frames

ABSTRACT The 137,036-bp plasmid pG8786 from rhamnose-positive Yersinia pestis G8786 isolated from the high mountainous Caucasian plague focus in Georgia is an enlarged form of the pFra virulence-associated plasmid containing genes for synthesis of the antigen fraction 1 and phospholipase D. In addition to the completely conserved genes of the pFra backbone, pG8786 contains two large regions consisting of 4,642 and 32,617 bp, designated regions 1 and 2, respectively. Region 1 retains a larger part of Salmonella enterica serovar Typhi plasmid pHCM2 resembling the backbone of pFra replicons, while region 2 contains 25 open reading frames with high levels of similarity to the transfer genes of the F-like plasmids. Surprisingly, region 1 is also present in the pFra plasmid of avirulent Y. pestis strain 91001 isolated in Inner Mongolia, People's Republic of China. Despite the fact that some genes typically involved in conjugative transfer of the F-like replicons are missing in pG8786, we cannot exclude the possibility that pG8786 might be transmissive under certain conditions. pG8786 seems to be an ancient form of the pFra group of plasmids that were conserved due to the strict geographical isolation of rhamnose-positive Y. pestis strains in the high mountainous Caucasian plague locus.

scholarly journals Papillomaviruses infecting cetaceans exhibit signs of genome adaptation following a recombination event

2020 ◽  
Vol 6 (1) ◽  
Author(s):  
Fanni Borvető ◽  
Ignacio G Bravo ◽  
Anouk Willemsen
Keyword(s):  
Recombination Event ◽  
Regulatory Element ◽  
Phylogenetic Analyses ◽  
Expression Patterns ◽  
Regulatory Region ◽  
Open Reading Frames ◽  
Host Switch ◽  
Regulatory Changes ◽  
Evolution Of Gene Regulation ◽  
Reading Frames

Abstract Papillomaviruses (PVs) have evolved through a complex evolutionary scenario where virus–host co-evolution alone is not enough to explain the phenotypic and genotypic PV diversity observed today. Other evolutionary processes, such as host switch and recombination, also appear to play an important role in PV evolution. In this study, we have examined the genomic impact of a recombination event between distantly related PVs infecting Cetartiodactyla (even-toed ungulates and cetaceans). Our phylogenetic analyses suggest that one single recombination was responsible for the generation of extant ‘chimeric’ PV genomes infecting cetaceans. By correlating the phylogenetic relationships to the genomic content, we observed important differences between the recombinant and non-recombinant cetartiodactyle PV genomes. Notably, recombinant PVs contain a unique set of conserved motifs in the upstream regulatory region (URR). We interpret these regulatory changes as an adaptive response to drastic changes in the PV genome. In terms of codon usage preferences (CUPrefs), we did not detect any particular differences between orthologous open reading frames in recombinant and non-recombinant PVs. Instead, our results are in line with previous observations suggesting that CUPrefs in PVs are rather linked to gene expression patterns as well as to gene function. We show that the non-coding URR of PVs infecting cetaceans, the central regulatory element in these viruses, exhibits signs of adaptation following a recombination event. Our results suggest that also in PVs, the evolution of gene regulation can play an important role in speciation and adaptation to novel environments.

scholarly journals Proteins encoded by Novel ORFs have increased disorder but can be biochemically regulated and harbour pathogenic mutations

2019 ◽  
Author(s):  
N. Suhas Jagannathan ◽  
Narendra Meena ◽  
Kethaki Prathivadi Bhayankaram ◽  
Sudhakaran Prabakaran
Keyword(s):  
Biological Function ◽  
Structural Disorder ◽  
Open Reading Frames ◽  
Deleterious Mutations ◽  
Computational Tools ◽  
Post Translational Modifications ◽  
Novel Proteins ◽  
Regulatory Changes ◽  
Reading Frames ◽  
Novel Protein

Abstract Recent advances in proteogenomics indicate that protein or protein-like products can be encoded by previously uncharacterized Open Reading Frames (ORFs) that we define as Novel Open Reading Frames (nORFs)1​ ​,2​ ​. Although it is yet unclear if these protein or protein-like products could possess any significant biological function hopes have been raised to target them for anticancer and antimicrobial therapy 3​ ,4​. In this study, we used computational tools to systematically investigate these novel protein sequences for their propensities toward structural disorder, post-translational modifications (PTM) and mutational densities. We found that these novel proteins have significantly higher disorder and similar PTM frequencies compared to known proteins. Although these regions were found to harbour deleterious mutations, we did not observe any correlation between the pathogenicity of mutations and their location (ordered/disordered) within these novel proteins. This study suggests that these nORFs encode an important class of proteins, that could undergo sequence, structural or regulatory changes during complex diseases, and hence warrant further study.

scholarly journals Sequence Analysis of Mus dunni Endogenous Virus Reveals a Hybrid VL30/Gibbon Ape Leukemia Virus-Like Structure and a Distinct Envelope

1998 ◽  
Vol 72 (9) ◽  
pp. 7459-7466 ◽  
Author(s):  
Greg Wolgamot ◽  
Lynn Bonham ◽  
A. Dusty Miller
Keyword(s):  
Leukemia Virus ◽  
Open Reading Frames ◽  
Cell Entry ◽  
Endogenous Virus ◽  
Entire Genome ◽  
Naturally Occurring ◽  
Gibbon Ape Leukemia Virus ◽  
Apparent Similarity ◽  
Packaging Sequence ◽  
Reading Frames

ABSTRACT Mus dunni endogenous virus (MDEV) can be activated fromM. dunni cells by exposing the cells to hydrocortisone or 5-iodo-2′-deoxyuridine. Interference analysis has revealed that MDEV uses a receptor for cell entry that is different from those used by other murine retroviruses. The entire genome has now been sequenced, revealing a long terminal repeat (LTR)-gag-pol-env-LTR structure typical of simple retroviruses of the murine leukemia virus genus, with no additional open reading frames between env and the 3′ LTR. The LTRs and other noncoding regions of MDEV are most closely related to those of VL30 elements, while the majority of the coding sequences are most closely related to those of gibbon ape leukemia virus. MDEV represents the first example of a naturally occurring, replication-competent virus with sequences closely related to VL30 elements. The U3 region of MDEV contains six nearly perfect 80-bp repeats and the beginning of a seventh, and the region expected to contain the packaging sequence contains approximately four imperfect 33-bp repeats. The receptor specificity domains of the envelope are unique among retroviruses and show no apparent similarity to regions of known proteins.

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