scholarly journals Complete Genomes of the Anaerobic Degradation Specialists Aromatoleum petrolei ToN1T and Aromatoleum bremense PbN1T

2021 ◽  
pp. 1-20
Author(s):  
Arne Weiten ◽  
Kristin Kalvelage ◽  
Patrick Becker ◽  
Richard Reinhardt ◽  
Thomas Hurek ◽  
...  
Keyword(s):  
Anaerobic Degradation ◽  
Gene Clusters ◽  
Secretion System ◽  
Specific Gene ◽  
High Plasticity ◽  
Related Genus ◽  
Functional Heterogeneity ◽  
High Similarity ◽  
Enzyme Maturation ◽  
Complete Genomes

The betaproteobacterial genus <i>Aromatoleum</i> comprises facultative denitrifiers specialized in the anaerobic degradation of recalcitrant organic compounds (aromatic and terpenoid). This study reports on the complete and manually annotated genomes of <i>Ar. petrolei</i> ToN1<sup>T</sup> (5.41 Mbp) and <i>Ar. bremense</i> PbN1<sup>T</sup> (4.38 Mbp), which cover the phylogenetic breadth of the genus <i>Aromatoleum</i> together with previously genome sequenced <i>Ar. aromaticum</i> EbN1<sup>T</sup> [Rabus et al., Arch Microbiol. 2005 Jan;183(1):27–36]. The gene clusters for the anaerobic degradation of aromatic and terpenoid (strain ToN1<sup>T</sup> only) compounds are scattered across the genomes of strains ToN1<sup>T</sup> and PbN1<sup>T</sup>. The richness in mobile genetic elements is shared with other <i>Aromatoleum</i> spp., substantiating that horizontal gene transfer should have been a major driver in shaping the genomes of this genus. The composite catabolic network of strains ToN1<sup>T</sup> and PbN1<sup>T</sup> comprises 88 proteins, the coding genes of which occupy 86.1 and 76.4 kbp (1.59 and 1.75%) of the respective genome. The strain-specific gene clusters for anaerobic degradation of ethyl-/propylbenzene (strain PbN1<sup>T</sup>) and toluene/monoterpenes (strain ToN1<sup>T</sup>) share high similarity with their counterparts in <i>Ar. aromaticum</i> strains EbN1<sup>T</sup> and pCyN1, respectively. Glucose is degraded via the ED-pathway in strain ToN1<sup>T</sup>, while gluconeogenesis proceeds via the reverse EMP-pathway in strains ToN1<sup>T</sup>, PbN1<sup>T</sup>, and EbN1<sup>T</sup>. The diazotrophic, endophytic lifestyle of closest related genus <i>Azoarcus</i> is known to be associated with nitrogenase and type-6 secretion system (T6SS). By contrast, strains ToN1<sup>T</sup>, PbN1<sup>T</sup>, and EbN1<sup>T</sup> lack <i>nif</i> genes for nitrogenase (including cofactor synthesis and enzyme maturation). Moreover, strains PbN1<sup>T</sup> and EbN1<sup>T</sup> do not possess <i>tss</i> genes for T6SS, while strain ToN1<sup>T</sup> does and facultative endophytic “<i>Aromatoleum</i>” sp. CIB is known to even have both. These findings underpin the functional heterogeneity among <i>Aromatoleum</i> members, correlating with the high plasticity of their genomes.

scholarly journals Virulence genes and previously unexplored gene clusters in four commensal Neisseria spp. isolated from the human throat expand the neisserial gene repertoire

2020 ◽  
Vol 6 (9) ◽  
Author(s):  
Alan Calder ◽  
Chukwuma Jude Menkiti ◽  
Aylin Çağdaş ◽  
Jefferson Lisboa Santos ◽  
Ricarda Streich ◽  
...  
Keyword(s):  
Type Species ◽  
Gene Clusters ◽  
Secretion System ◽  
Specific Gene ◽  
Gene Repertoire ◽  
Type Vi Secretion System ◽  
Content Type ◽  
Link Type ◽  
Type Iv ◽  
System A

Commensal non-pathogenic Neisseria spp. live within the human host alongside the pathogenic Neisseria meningitidis and Neisseria gonorrhoeae and due to natural competence, horizontal gene transfer within the genus is possible and has been observed. Four distinct Neisseria spp. isolates taken from the throats of two human volunteers have been assessed here using a combination of microbiological and bioinformatics techniques. Three of the isolates have been identified as Neisseria subflava biovar perflava and one as Neisseria cinerea . Specific gene clusters have been identified within these commensal isolate genome sequences that are believed to encode a Type VI Secretion System, a newly identified CRISPR system, a Type IV Secretion System unlike that in other Neisseria spp., a hemin transporter, and a haem acquisition and utilization system. This investigation is the first to investigate these systems in either the non-pathogenic or pathogenic Neisseria spp. In addition, the N. subflava biovar perflava possess previously unreported capsule loci and sequences have been identified in all four isolates that are similar to genes seen within the pathogens that are associated with virulence. These data from the four commensal isolates provide further evidence for a Neisseria spp. gene pool and highlight the presence of systems within the commensals with functions still to be explored.

scholarly journals Two Angular Dioxygenases Contribute to the Metabolic Versatility of Dibenzofuran-Degrading Rhodococcus sp. Strain HA01

2008 ◽  
Vol 74 (12) ◽  
pp. 3812-3822 ◽  
Author(s):  
Hamdy A. H. Aly ◽  
Nguyen B. Huu ◽  
Victor Wray ◽  
Howard Junca ◽  
Dietmar H. Pieper
Keyword(s):  
Angular Position ◽  
Gene Clusters ◽  
The Novel ◽  
High Similarity ◽  
Complementary Activity ◽  
Metabolic Versatility ◽  
Oxygenase Activity ◽  
Angular Dioxygenation ◽  
Low Activity ◽  
Rhodococcus Sp

ABSTRACT Rhodococcus sp. strain HA01, isolated through its ability to utilize dibenzofuran (DBF) as the sole carbon and energy source, was also capable, albeit with low activity, of transforming dibenzo-p-dioxin (DD). This strain could also transform 3-chlorodibenzofuran (3CDBF), mainly by angular oxygenation at the ether bond-carrying carbon (the angular position) and an adjacent carbon atom, to 4-chlorosalicylate as the end product. Similarly, 2-chlorodibenzofuran (2CDBF) was transformed to 5-chlorosalicylate. However, lateral oxygenation at the 3,4-positions was also observed and yielded the novel product 2-chloro-3,4-dihydro-3,4-dihydroxydibenzofuran. Two gene clusters encoding enzymes for angular oxygenation (dfdA1A2A3A4 and dbfA1A2) were isolated, and expression of both was observed during growth on DBF. Heterologous expression revealed that both oxygenase systems catalyze angular oxygenation of DBF and DD but exhibited complementary substrate specificity with respect to CDBF transformation. While DfdA1A2A3A4 oxygenase, with high similarity to DfdA1A2A3A4 oxygenase from Terrabacter sp. strain YK3, transforms 3CDBF by angular dioxygenation at a rate of 29% ± 4% that of DBF, 2CDBF was not transformed. In contrast, DbfA1A2 oxygenase, with high similarity to the DbfA1A2 oxygenase from Terrabacter sp. strain DBF63, exhibited complementary activity with angular oxygenase activity against 2CDBF but negligible activity against 3CDBF. Thus, Rhodococcus sp. strain HA01 constitutes the first described example of a bacterial strain where coexpression of two angular dioxygenases was observed. Such complementary activity allows for the efficient transformation of chlorinated DBFs.

scholarly journals The B-type lamin is required for somatic repression of testis-specific gene clusters

2009 ◽  
Vol 106 (9) ◽  
pp. 3282-3287 ◽  
Author(s):  
Y. Y. Shevelyov ◽  
S. A. Lavrov ◽  
L. M. Mikhaylova ◽  
I. D. Nurminsky ◽  
R. J. Kulathinal ◽  
...  
Keyword(s):  
Gene Clusters ◽  
Specific Gene

scholarly journals FoxP3 associates with enhancer-promoter loops to regulate Treg-specific gene expression

2021 ◽  
Author(s):  
Ricardo N Ramirez ◽  
Kaitavjeet Chowdhary ◽  
Juliette Leon ◽  
Diane Mathis ◽  
Christophe Benoist
Keyword(s):  
Gene Expression ◽  
Chromatin Immunoprecipitation ◽  
T Regulatory Cells ◽  
Gene Clusters ◽  
Specific Gene ◽  
Regulatory Cells ◽  
Proximity Ligation ◽  
The Core ◽  
Transcriptional Cofactors ◽  
Number Of Genes

Gene expression programs are specified by higher-order chromatin structure and enhancer-promoter loops (EPL). T regulatory cells (Treg) identity is dominantly specified by the transcription factor FoxP3, whose mechanism of action is unclear. We applied proximity-ligation with chromatin immunoprecipitation (HiChIP) in Treg and closely related conventional CD4+ T cells (Tconv). EPL identified by H3K27Ac HiChIP showed a range of connection intensity, with some super-connected genes. TF-specific HiChIP showed that FoxP3 interacts with EPLs at a large number of genes, including some not differentially expressed in Treg vs Tconv, but enriched at the core Treg signature loci that it upregulates. FoxP3 association correlates with heightened H3H27Ac looping, as ascertained by analysis of FoxP3-deficient Treg-like cells. There was marked asymmetry in the loci where FoxP3 associated at the enhancer- or the promoter-side of EPLs, with enrichment for different transcriptional cofactors. FoxP3 EPL intensity distinguished gene clusters identified by single-cell ATAC-seq as co-varying between individual Tregs, supporting a direct transactivation model for FoxP3 in determining Treg identity.

scholarly journals Fur-Dam Regulatory Interplay at an Internal Promoter of the Enteroaggregative Escherichia coli Type VI Secretion sci1 Gene Cluster

2020 ◽  
Vol 202 (10) ◽  
Author(s):  
Yannick R. Brunet ◽  
Christophe S. Bernard ◽  
Eric Cascales
Keyword(s):  
Escherichia Coli ◽  
Gene Cluster ◽  
Gene Clusters ◽  
Secretion System ◽  
Target Cells ◽  
Type Vi Secretion System ◽  
Content Type ◽  
Internal Promoter ◽  
E Coli ◽  
Type Vi Secretion

ABSTRACT The type VI secretion system (T6SS) is a weapon for delivering effectors into target cells that is widespread in Gram-negative bacteria. The T6SS is a highly versatile machine, as it can target both eukaryotic and prokaryotic cells, and it has been proposed that T6SSs are adapted to the specific needs of each bacterium. The expression of T6SS gene clusters and the activation of the secretion apparatus are therefore tightly controlled. In enteroaggregative Escherichia coli (EAEC), the sci1 T6SS gene cluster is subject to a complex regulation involving both the ferric uptake regulator (Fur) and DNA adenine methylase (Dam)-dependent DNA methylation. In this study, an additional, internal, promoter was identified within the sci1 gene cluster using +1 transcriptional mapping. Further analyses demonstrated that this internal promoter is controlled by a mechanism strictly identical to that of the main promoter. The Fur binding box overlaps the −10 transcriptional element and a Dam methylation site, GATC-32. Hence, the expression of the distal sci1 genes is repressed and the GATC-32 site is protected from methylation in iron-rich conditions. The Fur-dependent protection of GATC-32 was confirmed by an in vitro methylation assay. In addition, the methylation of GATC-32 negatively impacted Fur binding. The expression of the sci1 internal promoter is therefore controlled by iron availability through Fur regulation, whereas Dam-dependent methylation maintains a stable ON expression in iron-limited conditions. IMPORTANCE Bacteria use weapons to deliver effectors into target cells. One of these weapons, the type VI secretion system (T6SS), assembles a contractile tail acting as a spring to propel a toxin-loaded needle. Its expression and activation therefore need to be tightly regulated. Here, we identified an internal promoter within the sci1 T6SS gene cluster in enteroaggregative E. coli. We show that this internal promoter is controlled by Fur and Dam-dependent methylation. We further demonstrate that Fur and Dam compete at the −10 transcriptional element to finely tune the expression of T6SS genes. We propose that this elegant regulatory mechanism allows the optimum production of the T6SS in conditions where enteroaggregative E. coli encounters competing species.

scholarly journals Differential co-expression network analysis for identification of functional modules in HIV infection and tubercolosis-HIV co-infection

2016 ◽  
Vol 89 (2) ◽  
Author(s):  
Mohit Jha ◽  
Anvita Gupta ◽  
Sudha Singh ◽  
Khushhali Menaria Pandey
Keyword(s):  
Network Analysis ◽  
Hiv Infection ◽  
Enrichment Analysis ◽  
Gene Interaction ◽  
Gene Clusters ◽  
Functional Enrichment Analysis ◽  
Gene Expression Omnibus ◽  
Functional Enrichment ◽  
Specific Gene ◽  
Diagnostic Strategies

Co-infection with tuberculosis (TB) is the preeminent cause of demise in human immunodeficiency virus (HIV) infected individuals. However, diagnosis of TB, particularly in the presence of an HIV co-infection, can be limiting owing to the high inaccuracy associated with conventional diagnostic strategies. Here we determine dysregulated pathways in TB-HIV co-infection and HIV infection utilizing coexpression networks. Primarily, we utilized preservation statistics to identify gene modules that exhibit a weak conservation of network topology within HIV infected and TB-HIV co-infected networks. Raw data was downloaded from Gene Expression Omnibus (GSE50834) and duly pre-processed. Co-expression networks for each condition (HIV infected and TB-HIV co-infected) were constructed independently. Preservation of HIV infected network edges was evaluated with respect to TB-HIV co-infected and vice versa using weighted correlation network analysis. Two out of the 22 modules were identified as exhibiting weak preservation in both conditions. Functional enrichment analysis identified that weakly preserved modules were pertinent to the condition under study. For instance, weakly preserved TBHIV co-infected module T1 enriched for genes associated with mitochondrion exhibited the highest fraction of gene interaction pairs exclusive to TB-HIV co-infection. Concisely, we illustrated the application of using preservation statistics to detect modules functionally linked with dysregulated pathways in disease, as exemplified by the mitochondrion module T1. Our analyses discovered gene clusters that are non-randomly linked with the disease. Highly specific gene pairs pointed to interactions between known markers of disease and favoured identification of possible markers that are likely to be associated with the disease.

Identification of tissue-specific gene clusters and orthologues of nodulation-related genes in Vigna angularis

2014 ◽  
Vol 12 (S1) ◽  
pp. S21-S26 ◽  
Author(s):  
Yang Jae Kang ◽  
Jayern Lee ◽  
Yong Hwan Kim ◽  
Suk-Ha Lee
Keyword(s):  
De Novo ◽  
Transcriptome Assembly ◽  
Lotus Japonicus ◽  
Gene Clusters ◽  
Specific Gene ◽  
Vigna Angularis ◽  
Model Legume ◽  
Tissue Specific ◽  
Autoregulation Of Nodulation ◽  
Species Specific

Nitrogen fixation in legumes is an important agricultural trait that results from symbiosis between the root and rhizobia. To understand the molecular basis of nodulation, recent research has been focused on the identification of nodulation-related genes by functional analysis using two major model legumes, Medicago truncatula and Lotus japonicus. Thus far, three important processes have been discovered, namely Nod factor (NF) perception, NF signalling and autoregulation of nodulation. Nevertheless, application of the results of these studies is limited for non-model legume crops because a reference genome is unavailable. However, because the cost of whole-transcriptome analysis has dropped dramatically due to the Next generation sequencer (NGS) technology, minor crops for which reference sequences are yet to be constructed can still be studied at the genome level. In this study, we sequenced the leaf and root transcriptomes of Vigna angularis (accession IT213134) and de novo assembled. Our results demonstrate the feasibility of using the transcriptome assembly to effectively identify tissue-specific peptide clusters related to tissue-specific functions and species-specific nodulation-related genes.

scholarly journals Vibrio cholerae Requires the Type VI Secretion System Virulence Factor VasX To Kill Dictyostelium discoideum

2011 ◽  
Vol 79 (7) ◽  
pp. 2941-2949 ◽  
Author(s):  
Sarah T. Miyata ◽  
Maya Kitaoka ◽  
Teresa M. Brooks ◽  
Steven B. McAuley ◽  
Stefan Pukatzki
Keyword(s):  
Vibrio Cholerae ◽  
Dictyostelium Discoideum ◽  
Virulence Factor ◽  
Membrane Lipids ◽  
Gene Clusters ◽  
Secretion System ◽  
Type Vi Secretion System ◽  
Content Type ◽  
Enzymatic Function ◽  
Type Vi Secretion

ABSTRACTThe type VI secretion system (T6SS) is recognized as an important virulence mechanism in several Gram-negative pathogens. InVibrio cholerae, the causative agent of the diarrheal disease cholera, a minimum of three gene clusters—one main cluster and two auxiliary clusters—are required to form a functional T6SS apparatus capable of conferring virulence toward eukaryotic and prokaryotic hosts. Despite an increasing understanding of the components that make up the T6SS apparatus, little is known about the regulation of these genes and the gene products delivered by this nanomachine. VasH is an important regulator of theV. choleraeT6SS. Here, we present evidence that VasH regulates the production of a newly identified protein, VasX, which in turn requires a functional T6SS for secretion. Deletion ofvasXdoes not affect export or enzymatic function of the structural T6SS proteins Hcp and VgrG-1, suggesting that VasX is dispensable for the assembly of the physical translocon complex. VasX localizes to the bacterial membrane and interacts with membrane lipids. We present VasX as a novel virulence factor of the T6SS, as aV. choleraemutant lackingvasXexhibits a phenotype of attenuated virulence towardDictyostelium discoideum.

scholarly journals Live, Attenuated Coronavirus Vaccines through the Directed Deletion of Group-Specific Genes Provide Protection against Feline Infectious Peritonitis

2004 ◽  
Vol 78 (8) ◽  
pp. 3863-3871 ◽  
Author(s):  
Bert Jan Haijema ◽  
Haukeline Volders ◽  
Peter J. M. Rottier
Keyword(s):  
Neutralizing Antibodies ◽  
Reverse Genetics ◽  
Clinical Symptoms ◽  
Gene Clusters ◽  
Wild Type Virus ◽  
Specific Gene ◽  
Gene Deletions ◽  
Reading Frame ◽  
Feline Infectious Peritonitis ◽  
Homologous Challenge

ABSTRACT Feline infectious peritonitis (FIP) is a fatal immunity-mediated disease caused by mutants of a ubiquitous coronavirus. Since previous attempts to protect cats under laboratory and field conditions have been largely unsuccessful, we used our recently developed system of reverse genetics (B. J. Haijema, H. Volders, and P. J. M. Rottier, J. Virol. 77:4528-4538, 2003) for the development of a modified live FIP vaccine. With this objective, we deleted the group-specific gene cluster open reading frame 3abc or 7ab and obtained deletion mutant viruses that not only multiplied well in cell culture but also showed an attenuated phenotype in the cat. At doses at which the wild-type virus would be fatal, the mutants with gene deletions did not cause any clinical symptoms. They still induced an immune response, however, as judged from the high levels of virus-neutralizing antibodies. The FIP virus (FIPV) mutant lacking the 3abc cluster and, to a lesser extent, the mutant missing the 7ab cluster, protected cats against a lethal homologous challenge; no protection was obtained with the mutant devoid of both gene clusters. Our studies show that the deletion of group-specific genes from the coronavirus genome results in live attenuated candidate vaccines against FIPV. More generally, our approach may allow the development of vaccines against infections with other pathogenic coronaviruses, including that causing severe acute respiratory syndrome in humans.

scholarly journals The Chlamydia pneumoniae Type III Secretion-Related lcrH Gene Clusters Are Developmentally Expressed Operons

2005 ◽  
Vol 187 (22) ◽  
pp. 7853-7856 ◽  
Author(s):  
Scot P. Ouellette ◽  
Yasser M. AbdelRahman ◽  
Robert J. Belland ◽  
Gerald I. Byrne
Keyword(s):  
Type Iii Secretion ◽  
Sigma Factor ◽  
Chlamydia Pneumoniae ◽  
Developmental Regulation ◽  
Gene Clusters ◽  
Secretion System ◽  
Structural Components ◽  
Separate Gene ◽  
Type Iii ◽  
Regulation Mechanisms

ABSTRACT Two chlamydial homologues of the Yersinia lcrH chaperone for type III secretion system structural components are present within separate gene clusters. Quantitative transcriptional analyses demonstrated that each cluster is differentially regulated and expressed as an operon using major sigma factor elements, suggesting the presence of more elaborate developmental regulation mechanisms in chlamydiae.

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