scholarly journals cis-Encoded Small RNAs, a Conserved Mechanism for Repression of Polysaccharide Utilization in Bacteroides

2016 ◽  
Vol 198 (18) ◽  
pp. 2410-2418 ◽  
Author(s):  
Yanlu Cao ◽  
Konrad U. Förstner ◽  
Jörg Vogel ◽  
C. Jeffrey Smith
Keyword(s):  
Small Rnas ◽  
Nutritive Value ◽  
Hierarchical Control ◽  
Gene Clusters ◽  
Regulatory Control ◽  
Energy Sources ◽  
Transcriptional Level ◽  
Human Gut ◽  
Content Type ◽  
Wide Range

ABSTRACTBacteroidesis a major component of the human gut microbiota which has a broad impact on the development and physiology of its host and a potential role in a wide range of disease syndromes. The predominance of this genus is due in large part to expansion of paralogous gene clusters, termedpolysaccharideutilizationloci (PULs), dedicated to the uptake and catabolism of host-derived and dietary polysaccharides. The nutritive value and availability of polysaccharides in the gut vary greatly; thus, their utilization is hierarchical and strictly controlled. A typical PUL includes regulatory genes that induce PUL expression in response to the presence of specific glycan substrates. However, the existence of additional regulatory mechanisms has been predicted to explain phenomena such as hierarchical control and catabolite repression. In this report, a previously unknown layer of regulatory control was discovered inBacteroides fragilis. Exploratory transcriptome sequencing (RNA-seq) analysis revealed the presence ofcis-encoded antisense small RNAs (sRNAs) associated with 15 (30%) of theB. fragilisPULs. A model system using the Don (degradation of N-glycans) PUL showed that thedonSsRNA negatively regulated Don expression at the transcriptional level, resulting in a decrease in N-glycan utilization. Additional studies performed with otherBacteroidesspecies indicated that this regulatory mechanism is highly conserved and, interestingly, that the regulated PULs appear to be closely linked to the utilization of host-derived glycans rather than dietary plant polysaccharides. The findings described here demonstrate a global control mechanism underlying known PUL regulatory circuits and provide insight into regulation ofBacteroidesphysiology.IMPORTANCEThe human gut is colonized by a dense microbiota which is essential to the health and normal development of the host. A key to gut homeostasis is the preservation of a stable, diverse microbiota.Bacteroidesis a dominant genus in the gut, and the ability ofBacteroidesspecies to efficiently compete for a wide range of glycan energy sources is a crucial advantage for colonization. Glycan utilization is mediated by a large number ofpolysaccharideutilizationloci (PULs) which are regulated by substrate induction. In this report, a novel family of antisense sRNAs is described whose members repress gene expression in a distinct subset of PULs. This repression downregulates PUL expression in the presence of energy sources that are more readily utilized such as glucose, thereby allowing efficient glycan utilization.

scholarly journals Xylan degradation by the human gut Bacteroides xylanisolvens XB1AT involves two distinct gene clusters that are linked at the transcriptional level

BMC Genomics ◽  
2016 ◽  
Vol 17 (1) ◽  
Author(s):  
Jordane Despres ◽  
Evelyne Forano ◽  
Pascale Lepercq ◽  
Sophie Comtet-Marre ◽  
Gregory Jubelin ◽  
...  
Keyword(s):  
Gene Clusters ◽  
Transcriptional Level ◽  
Human Gut ◽  
Xylan Degradation ◽  
Distinct Gene

scholarly journals Additional Og-Typing PCR Techniques Targeting Escherichia coli-Novel and Shigella-Unique O-Antigen Biosynthesis Gene Clusters

2020 ◽  
Vol 58 (11) ◽  
Author(s):  
Atsushi Iguchi ◽  
Hironobu Nishii ◽  
Kazuko Seto ◽  
Jiro Mitobe ◽  
Kenichi Lee ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Strong Association ◽  
Gene Clusters ◽  
Epidemiological Studies ◽  
Content Type ◽  
E Coli ◽  
O Antigen ◽  
Wide Range ◽  
Biosynthesis Gene ◽  
Almost All

ABSTRACT The O-serogrouping of pathogenic Escherichia coli is a standard method for subtyping strains for epidemiological studies and controls. O-serogroup diversification shows a strong association with the genetic diversity in some O-antigen biosynthesis gene clusters. Through genomic studies, in addition to the types of O-antigen biosynthesis gene clusters (Og-types) from conventional O-serogroup strains, a number of novel Og-types have been found in E. coli isolates. To assist outbreak investigations and surveillance of pathogenic E. coli at inspection institutes, in previous studies, we developed PCR methods that could determine almost all conventional O-serogroups and some novel Og-types. However, there are still many Og-types that may not be determined by simple genetic methods such as PCR. Thus, in the present study, we aimed to develop an additional Og-typing PCR system. Based on the novel Og-types, including OgN32, OgN33, and OgN34, presented in this study, we designed an additional 24 PCR primer pairs targeting 14 novel and 2 diversified E. coli Og-types and 8 Shigella-unique Og-types. Subsequently, we developed 5 new multiplex PCR sets consisting of 33 primers, including the aforementioned 24 primers and 9 primers reported in previous studies. The accuracy and specificity of the PCR system was validated using approximately 260 E. coli and Shigella O-serogroup and Og-type reference strains. The Og-typing PCR system reported here can determine a wide range of Og-types of E. coli and may help epidemiological studies, in addition to the surveillance of pathogenic E. coli.

scholarly journals A Novel AdpA Homologue Negatively Regulates Morphological Differentiation inStreptomyces xiamenensis318

2019 ◽  
Vol 85 (7) ◽  
Author(s):  
Xu-Liang Bu ◽  
Jing-Yi Weng ◽  
Bei-Bei He ◽  
Min-Juan Xu ◽  
Jun Xu
Keyword(s):  
Cell Growth ◽  
Secondary Metabolism ◽  
Gene Cluster ◽  
Morphological Differentiation ◽  
Gene Clusters ◽  
Transcriptional Level ◽  
Negative Effects ◽  
Promoter Regions ◽  
Content Type ◽  
Enhanced Production

ABSTRACTThe pleiotropic transcriptional regulator AdpA positively controls morphological differentiation and regulates secondary metabolism in mostStreptomycesspecies.Streptomyces xiamenensis318 has a linear chromosome 5.96 Mb in size. How AdpA affects secondary metabolism and morphological differentiation in such a naturally minimized genomic background is unknown. Here, we demonstrated that AdpASx, an AdpA orthologue inS. xiamenensis, negatively regulates cell growth and sporulation and bidirectionally regulates the biosynthesis of xiamenmycin and polycyclic tetramate macrolactams (PTMs) inS. xiamenensis318. Overexpression of theadpASxgene inS. xiamenensis318 had negative effects on morphological differentiation and resulted in reduced transcription of putativessgA,ftsZ,ftsH,amfC,whiB,wblA1,wblA2,wblE, and a gene encoding sporulation-associated protein (sxim_29740), whereas the transcription of putativebldDandbldAgenes was upregulated. Overexpression ofadpASxled to significantly enhanced production of xiamenmycin but had detrimental effects on the production of PTMs. As expected, the transcriptional level of theximgene cluster was upregulated, whereas the PTM gene cluster was downregulated. Moreover, AdpASxnegatively regulated the transcription of its own gene. Electrophoretic mobility shift assays revealed that AdpASxcan bind the promoter regions of structural genes of both theximand PTM gene clusters as well as to the promoter regions of genes potentially involved in the cell growth and differentiation ofS. xiamenensis318. We report that an AdpA homologue has negative effects on morphological differentiation inS. xiamenensis318, a finding confirmed when AdpASxwas introduced into the heterologous hostStreptomyces lividansTK24.IMPORTANCEAdpA is a key regulator of secondary metabolism and morphological differentiation inStreptomycesspecies. However, AdpA had not been reported to negatively regulate morphological differentiation. Here, we characterized the regulatory role of AdpASxinStreptomyces xiamenensis318, which has a naturally streamlined genome. In this strain, AdpASxnegatively regulated cell growth and morphological differentiation by directly controlling genes associated with these functions. AdpASxalso bidirectionally controlled the biosynthesis of xiamenmycin and PTMs by directly regulating their gene clusters rather than through other regulators. Our findings provide additional evidence for the versatility of AdpA in regulating morphological differentiation and secondary metabolism inStreptomyces.

scholarly journals Functional Operons in Secondary Metabolic Gene Clusters in Glarea lozoyensis (Fungi, Ascomycota, Leotiomycetes)

mBio ◽  
2015 ◽  
Vol 6 (3) ◽  
Author(s):  
Qun Yue ◽  
Li Chen ◽  
Yan Li ◽  
Gerald F. Bills ◽  
Xinyu Zhang ◽  
...  
Keyword(s):  
Secondary Metabolism ◽  
Polyketide Synthase ◽  
Gene Clusters ◽  
Transcriptional Level ◽  
Tetramic Acid ◽  
Protein Coding ◽  
Content Type ◽  
Eukaryotic Gene ◽  
Transcriptional Units ◽  
Gene Structures

ABSTRACT Operons are multigene transcriptional units which occur mostly in prokaryotes but rarely in eukaryotes. Protein-coding operons have not been reported in the Fungi even though they represent a very diverse kingdom of organisms. Here, we report a functional operon involved in the secondary metabolism of the fungus Glarea lozoyensis belonging to Leotiomycetes (Ascomycota). Two contiguous genes, glpks3 and glnrps7, encoding polyketide synthase and nonribosomal peptide synthetase, respectively, are cotranscribed into one dicistronic mRNA under the control of the same promoter, and the mRNA is then translated into two individual proteins, GLPKS3 and GLNRPS7. Heterologous expression in Aspergillus nidulans shows that the GLPKS3-GLNRPS7 enzyme complex catalyzes the biosynthesis of a novel pyrrolidinedione-containing compound, xenolozoyenone (compound 1), which indicates the operon is functional. Although it is structurally similar to prokaryotic operons, the glpks3-glnrps7 operon locus has a monophylogenic origin from fungi rather than having been horizontally transferred from prokaryotes. Moreover, two additional operons, glpks28-glnrps8 and glpks29-glnrps9, were verified at the transcriptional level in the same fungus. This is the first report of protein-coding operons in a member of the Fungi. IMPORTANCE Operons are multigene transcriptional units which occur mostly in prokaryotes but rarely in eukaryotes. Three operon-like gene structures for secondary metabolism that were discovered in the filamentous fungus Glarea lozoyensis are the first examples of protein-coding operons identified in a member of the Fungi. Among them, the glpks3-glnrps7 operon is responsible for the biosynthesis of xenolozoyenone, which is a novel tetramic acid-containing compound. Although structurally similar to prokaryotic operons, the glpks3-glnrps7 operon locus did not result from horizontal gene transfer from prokaryotes. In addition, operonlike structures have been predicted in silico to be common in other fungi. The common occurrence and operonlike structure in fungi provide evolutionary insight and essential data for eukaryotic gene transcription.

Ecological houses of Southern Kazakhstan using renewable energy sources

2021 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Ardasher Namazbay Yussupov ◽  
Akmaral Ardasherovna Yussupova
Keyword(s):  
Renewable Energy ◽  
Rural Areas ◽  
Building Materials ◽  
Residential Buildings ◽  
Renewable Energy Sources ◽  
Local Population ◽  
Climatic Conditions ◽  
Energy Sources ◽  
Content Type ◽  
Wide Range

PurposeThe purpose of this article discusses the design of underground eco-houses using a dome structure of light construction while taking into account the historical experience of the development of the local population. This article considered the traditions of folk architecture and modern sophistication in the creation of energy-efficient eco-houses in foreign countries in the context of architecture and construction of affordable residential homes for the local population.Design/methodology/approachThe research presented in this paper was motivated by the need for developing agro-tourism facilities in hard-to-reach areas of the Silk Road in Southern Kazakhstan causes the construction of eco-houses built using local construction materials. Since ancient times in Southern Kazakhstan and during seasonal migrations in yurts of light construction, people have lived in mud-brick houses deep in the ground. Along with architectural and artistic solutions in building construction, great importance was attached to saving material resources, labour costs and achieving heat stability of residential buildings.FindingsIn the architectural and planning solution of the eco¬-house, progressive directions of construction of agrotechnical structures using renewable energy sources are adopted. Particular importance was given to the choice of the construction site on an elevated area nearby historical monuments and a favourable season for the construction of eco-houses with considering the natural and climatic characteristics of rural areas of Southern Kazakhstan.Research limitations/implicationsThis paper discussed the issues of insulation, ventilation and improving the eco-house microclimate comfort using local building materials. Improving the architectural and artistic expressiveness of the eco-house in terms of the tradition of folk architecture was also explicitly discussed in this paper.Practical implicationsTables with the justification of expediency of construction of economical eco-houses in natural and climatic conditions of Kazakhstan and Central Asia are provided. The results help to improve the energy efficiency of eco-houses in Kazakhstan by using renewable energy sources.Social implicationsSocial benefits are associated with the use of local raw materials. Eco-houses built from traditional building materials can become accessible to a wide range of people and stimulate the development of small businesses. This may be associated with the construction of eco-houses to serve visiting tourists in remote picturesque oases, as well as the manufacture of dome structures, felt products and the preparation of reed panels and so on.Originality/valueThe thermotechnical characteristics of the region's ground energy are given, which can significantly save the cost of heating the eco-house. Solutions for optimal insolation, ventilation of the eco-house are provided, taking into account the natural and climatic conditions of Southern Kazakhstan.

Epigenetic regulation of kallikrein-related peptidases: there is a whole new world out there

2012 ◽  
Vol 393 (5) ◽  
pp. 319-330 ◽  
Author(s):  
Maria D. Pasic ◽  
Ekaterina Olkhov ◽  
Bharati Bapat ◽  
George M. Yousef
Keyword(s):  
Epigenetic Regulation ◽  
Small Rnas ◽  
Experimental Validation ◽  
Target Prediction ◽  
Transcriptional Level ◽  
Potential Contribution ◽  
Epigenetic Changes ◽  
Disease Biomarkers ◽  
Essential Step ◽  
Wide Range

AbstractThe human kallikreins are a cluster of 15 kallikreins and kallikrein-related peptidases (KLKs). Evidence shows the involvement of KLKs in a wide range of pathophysiological processes, and underscores their potential contribution to cancer, skin and neurodegenerative disorders. The control ofKLKexpression is not fully elucidated. Understanding the mechanisms controllingKLKexpression is an essential step towards exploring the pathogenesis of several diseases and the use of KLKs as disease biomarkers and/or therapeutic targets. Recently, epigenetic changes (including methylation, histone modification and microRNAs [miRNAs]) have drawn attention as a new dimension for controllingKLKexpression. Reports showed the effect of methylation on the expression ofKLKgenes. This was also shown to have potential utility as a prognostic marker in cancer. miRNAs are small RNAs that control the expression of their targets at the post-transcriptional level. Target prediction showed that KLKs are potential targets of miRNAs that are dysregulated in tumors, including prostate, kidney and ovarian cancers, with downstream effect on tumor proliferation. Experimental validation remains an essential step to confirm the KLK-miRNA interaction. Epigenetic regulation of KLKs holds promise for an array of therapeutic applications in many diseases including cancer.

scholarly journals Draft Genome Assembly of the Entomopathogenic Bacterium Photorhabdus luminescens subsp. sonorensis Caborca

2019 ◽  
Vol 8 (36) ◽  
Author(s):  
Duy An Duong ◽  
Patricia Espinosa-Artiles ◽  
Rousel A. Orozco ◽  
István Molnár ◽  
S. Patricia Stock
Keyword(s):  
Secondary Metabolism ◽  
Genome Assembly ◽  
Draft Genome ◽  
Gene Clusters ◽  
Insect Species ◽  
Photorhabdus Luminescens ◽  
Putative Gene ◽  
Content Type ◽  
Draft Genome Assembly ◽  
Wide Range

Photorhabdus luminescens subsp. sonorensis strain Caborca is an entomopathogenic bacterium with a dual lifestyle, namely, as a mutualist of the Heterorhabditis sonorensis nematode and a pathogen to a wide range of insect species. The genome assembly, in 231 contigs, is 5.2 Mbp long and includes 25 putative gene clusters for secondary metabolism.

scholarly journals A Novel Angular Dioxygenase Gene Cluster Encoding 3-Phenoxybenzoate 1′,2′-Dioxygenase in Sphingobium wenxiniae JZ-1

2014 ◽  
Vol 80 (13) ◽  
pp. 3811-3818 ◽  
Author(s):  
Chenghong Wang ◽  
Qing Chen ◽  
Rui Wang ◽  
Chao Shi ◽  
Xin Yan ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Heme Iron ◽  
Transcriptional Level ◽  
Content Type ◽  
Type Iv ◽  
Reductase Gene ◽  
Wide Range ◽  
Dioxygenase Gene ◽  
Sphingomonas Wittichii ◽  
Angular Dioxygenase

ABSTRACTSphingobium wenxiniaeJZ-1 utilizes a wide range of pyrethroids and their metabolic product, 3-phenoxybenzoate, as sources of carbon and energy. A mutant JZ-1 strain, MJZ-1, defective in the degradation of 3-phenoxybenzoate was obtained by successive streaking on LB agar. Comparison of the draft genomes of strains JZ-1 and MJZ-1 revealed that a 29,366-bp DNA fragment containing a putative angular dioxygenase gene cluster (pbaA1A2B) is missing in strain MJZ-1. PbaA1, PbaA2, and PbaB share 65%, 52%, and 10% identity with the corresponding α and β subunits and the ferredoxin component of dioxin dioxygenase fromSphingomonas wittichiiRW1, respectively. Complementation ofpbaA1A2Bin strain MJZ-1 resulted in the active 3-phenoxybenzoate 1′,2′-dioxygenase, but the enzyme activity inEscherichia coliwas achieved only through the coexpression ofpbaA1A2Band a glutathione reductase (GR)-type reductase gene,pbaC, indicating that the 3-phenoxybenzoate 1′,2′-dioxygenase belongs to a type IV Rieske non-heme iron aromatic ring-hydroxylating oxygenase system consisting of a hetero-oligomeric oxygenase, a [2Fe-2S]-type ferredoxin, and a GR-type reductase. ThepbaCgene is not located in the immediate vicinity ofpbaA1A2B. 3-Phenoxybenzoate 1′,2′-dioxygenase catalyzes the hydroxylation in the 1′ and 2′ positions of the benzene moiety of 3-phenoxybenzoate, yielding 3-hydroxybenzoate and catechol. Transcription ofpbaA1A2BandpbaCwas induced by 3-phenoxybenzoate, but the transcriptional level ofpbaCwas far less than that ofpbaA1A2B, implying the possibility that PbaC may not be the only reductase that can physiologically transfer electrons to PbaA1A2B in strain JZ-1. Some GR-type reductases from other sphingomonad strains could also transfer electrons to PbaA1A2B, suggesting that PbaA1A2B has a low specificity for reductase.

scholarly journals The Leucine-Responsive Regulatory Protein Lrp Participates in Virulence Regulation Downstream of Small RNA ArcZ inErwinia amylovora

mBio ◽  
2019 ◽  
Vol 10 (3) ◽  
Author(s):  
Jeffrey K. Schachterle ◽  
George W. Sundin
Keyword(s):  
Small Rna ◽  
Transcriptional Activation ◽  
Fire Blight ◽  
Erwinia Amylovora ◽  
Regulatory Protein ◽  
Regulatory Control ◽  
Transcriptional Level ◽  
Content Type ◽  
Virulence Regulation ◽  
Blight Disease

ABSTRACTErwinia amylovoracauses the devastating fire blight disease of apple and pear trees. During systemic infection of host trees, pathogen cells must rapidly respond to changes in their environment as they move through different host tissues that present distinct challenges and sources of nutrition. Growing evidence indicates that small RNAs (sRNAs) play an important role in disease progression as posttranscriptional regulators. The sRNA ArcZ positively regulates the motility phenotype and transcription of flagellar genes inE. amylovoraEa1189 yet is a direct repressor of translation of the flagellar master regulator, FlhD. We utilized transposon mutagenesis to conduct a forward genetic screen and identified suppressor mutations that increase motility in the Ea1189ΔarcZmutant background. This enabled us to determine that the mechanism of transcriptional activation of theflhDCmRNA by ArcZ is mediated by the leucine-responsive regulatory protein, Lrp. We show that Lrp contributes to expression of virulence and several virulence-associated traits, including production of the exopolysaccharide amylovoran, levansucrase activity, and biofilm formation. We further show that Lrp is regulated posttranscriptionally by ArcZ through destabilization oflrpmRNA. Thus, ArcZ regulation of FlhDC directly and indirectly through Lrp forms an incoherent feed-forward loop that regulates levansucrase activity and motility as outputs. This work identifies Lrp as a novel participant in virulence regulation inE. amylovoraand places it in the context of a virulence-associated regulatory network.IMPORTANCEFire blight disease continues to plague the commercial production of apples and pears despite more than a century of research into disease epidemiology and disease control. The causative agent of fire blight,Erwinia amylovoracoordinates turning on or off specific virulence-associated traits at the appropriate time during disease development. The development of novel control strategies requires an in-depth understanding ofE. amylovoraregulatory mechanisms, including regulatory control of virulence-associated traits. This study investigates how the small RNA ArcZ regulates motility at the transcriptional level and identifies the transcription factor Lrp as a novel participant in the regulation of several virulence-associated traits. We report that ArcZ and Lrp together affect key virulence-associated traits through integration of transcriptional and posttranscriptional mechanisms. Further understanding of the topology of virulence regulatory networks can uncover weak points that can subsequently be exploited to controlE. amylovora.

scholarly journals Genomic and Chemical Diversity of Bacillus subtilis Secondary Metabolites against Plant Pathogenic Fungi

mSystems ◽  
2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Heiko T. Kiesewalter ◽  
Carlos N. Lozano-Andrade ◽  
Mario Wibowo ◽  
Mikael L. Strube ◽  
Gergely Maróti ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Secondary Metabolites ◽  
Pathogenic Fungus ◽  
Gene Clusters ◽  
Chemical Diversity ◽  
Biosynthetic Gene ◽  
Nonribosomal Peptide ◽  
Content Type ◽  
Wide Range

ABSTRACT Bacillus subtilis produces a wide range of secondary metabolites providing diverse plant growth-promoting and biocontrol abilities. These secondary metabolites include nonribosomal peptides with strong antimicrobial properties, causing either cell lysis, pore formation in fungal membranes, inhibition of certain enzymes, or bacterial protein synthesis. However, the natural products of B. subtilis are mostly studied either in laboratory strains or in individual isolates, and therefore, a comparative overview of secondary metabolites from various environmental B. subtilis strains is missing. In this study, we isolated 23 B. subtilis strains from 11 sampling sites, compared the fungal inhibition profiles of wild types and their nonribosomal peptide mutants, followed the production of targeted lipopeptides, and determined the complete genomes of 13 soil isolates. We discovered that nonribosomal peptide production varied among B. subtilis strains coisolated from the same soil samples. In vitro antagonism assays revealed that biocontrol properties depend on the targeted plant pathogenic fungus and the tested B. subtilis isolate. While plipastatin alone is sufficient to inhibit Fusarium spp., a combination of plipastatin and surfactin is required to hinder growth of Botrytis cinerea. Detailed genomic analysis revealed that altered nonribosomal peptide production profiles in specific isolates are due to missing core genes, nonsense mutation, or potentially altered gene regulation. Our study combines microbiological antagonism assays with chemical nonribosomal peptide detection and biosynthetic gene cluster predictions in diverse B. subtilis soil isolates to provide a broader overview of the secondary metabolite chemodiversity of B. subtilis. IMPORTANCE Secondary or specialized metabolites with antimicrobial activities define the biocontrol properties of microorganisms. Members of the Bacillus genus produce a plethora of secondary metabolites, of which nonribosomally produced lipopeptides in particular display strong antifungal activity. To facilitate the prediction of the biocontrol potential of new Bacillus subtilis isolates, we have explored the in vitro antifungal inhibitory profiles of recent B. subtilis isolates, combined with analytical natural product chemistry, mutational analysis, and detailed genome analysis of biosynthetic gene clusters. Such a comparative analysis helped to explain why selected B. subtilis isolates lack the production of certain secondary metabolites.

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