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 The application of the CRISPR–Cas9 system in Pseudomonas syringae pv. actinidiae

2020 ◽  
Vol 69 (3) ◽  
pp. 478-486
Author(s):  
Joycelyn Ho ◽  
Min Zhao ◽  
Samuel Wojcik ◽  
George Taiaroa ◽  
Margi Butler ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Type Species ◽  
Bacterial Pathogen ◽  
Specific Gene ◽  
Content Type ◽  
E Coli ◽  
Link Type ◽  
System A ◽  
Integrative Conjugative Element ◽  
Cas9 Protein

Introduction. Pseudomonas syringae pv. actinidiae (Psa) has emerged as a major bacterial pathogen of kiwifruit cultivation throughout the world. Aim. We aim to introduce a CRISPR–Cas9 system, a commonly used genome editing tool, into Psa. The protocols may also be useful in other Pseudomonas species. Methodology. Using standard molecular biology techniques, we modified plasmid pCas9, which carries the CRISPR–Cas9 sequences from Streptococcus pyogenes, for use in Psa. The final plasmid, pJH1, was produced in a series of steps and is maintained with selection in both Escherichia coli and Psa. Results. We have constructed plasmids carrying a CRISPR–Cas9 system based on that of S. pyogenes , which can be maintained, under selection, in Psa. We have shown that the gene targeting capacity of the CRISPR–Cas9 system is active and that the Cas9 protein is able to cleave the targeted sites. The Cas9 was directed to several different sites in the P. syringae genome. Using Cas9 we have generated Psa transformants that no longer carry the native plasmid present in Psa, and other transformants that lack the integrative, conjugative element, Pac_ICE1. Targeting of a specific gene, a chromosomal non-ribosomal peptide synthetase, led to gene knockouts with the transformants having deletions encompassing the target site. Conclusion. We have constructed shuttle plasmids carrying a CRISPR–Cas9 system that are maintained in both E. coli and P. syringae pv. actinidiae. We have used this gene editing system to eliminate features of the accessory genome (plasmids or ICEs) from Psa and to target a single chromosomal gene.

Roseomonas oleicola sp. nov., isolated from an oil production mixture in Yumen Oilfield, and emended description of Roseomonas frigidaquae

2021 ◽  
Vol 71 (10) ◽  
Author(s):  
Danni Wu ◽  
Hongcan Liu ◽  
Yuguang Zhou ◽  
Xiaolei Wu ◽  
Yong Nie ◽  
...  
Keyword(s):  
Type Species ◽  
Genomic Analysis ◽  
Oil Production ◽  
Gene Families ◽  
Specific Gene ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Content Type ◽  
Link Type ◽  
Type Strains

A pink, ovoid-shaped, Gram-stain-negative, strictly aerobic and motile bacterial strain, designated ROY-5-3T, was isolated from an oil production mixture from Yumen Oilfield in PR China. The strain grew at 4–42 °C (optimum, 30 °C), at pH 5–10 (optimum, 7) and with 0–5 % (w/v) NaCl (optimum, 0%). The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that ROY-5-3T belongs to the genus Roseomonas and shared the highest pairwise similarities with Roseomonas frigidaquae CW67T (98.1%), Roseomonas selenitidurans BU-1T (97.8%), Roseomonas tokyonensis K-20T (97.7%) and Roseomonas stagni HS-69T (97.3%). The average nucleotide identity and digital DNA–DNA hybridization values between ROY-5-3T and other related type strains of Roseomonas species were less than 84.08 and 28.60 %, respectively, both below the species delineation threshold. Pan-genomic analysis showed that the novel isolate ROY-5-3T shared 3265 core gene families with the four closely related type strains in Roseomonas , and the number of strain-specific gene families was 513. The major fatty acids were identified as summed feature 8 (C18 : 1 ω6c/C18 : 1 ω7c), summed feature 3 (C16 : 1 ω6c/C16 : 1 ω7c) and C16 : 0. Strain ROY-5-3T contained Q-10 as the main ubiquinone and the genomic DNA G+C content was 69.8 mol%. The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and phosphatidylglycerol. Based on the phylogenetic, morphological, physiological, chemotaxonomic and genome analyses, strain ROY-5-3T represents a novel species of the genus Roseomonas for which the name Roseomonas oleicola sp. nov. is proposed. The type strain is ROY-5-3T (=CGMCC 1.13459T =KCTC 82484T).

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 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 Lipopolysaccharide core type diversity in the Escherichia coli species in association with phylogeny, virulence gene repertoire and distribution of type VI secretion systems

2021 ◽  
Vol 7 (9) ◽  
Author(s):  
Sébastien O. Leclercq ◽  
Maxime Branger ◽  
David G. E. Smith ◽  
Pierre Germon
Keyword(s):  
Escherichia Coli ◽  
Type Species ◽  
Virulence Gene ◽  
Uneven Distribution ◽  
Gene Repertoire ◽  
Content Type ◽  
E Coli ◽  
Link Type ◽  
Wide Range ◽  
K 12

Escherichia coli is a very versatile species for which diversity has been explored from various perspectives highlighting, for example, phylogenetic groupings and pathovars, as well as a wide range of O serotypes. The highly variable O-antigen, the most external part of the lipopolysaccharide (LPS) component of the outer membrane of E. coli , is linked to the innermost lipid A through the core region of LPS of which five different structures, denominated K-12, R1, R2, R3 and R4, have been characterized so far. The aim of the present study was to analyse the prevalence of these LPS core types in the E. coli species and explore their distribution in the different E. coli phylogenetic groups and in relationship with the virulence gene repertoire. Results indicated an uneven distribution of core types between the different phylogroups, with phylogroup A strains being the most diverse in terms of LPS core types, while phylogroups B1, D and E strains were dominated by the R3 type, and phylogroups B2 and C strains were dominated by the R1 type. Strains carrying the LEE virulence operon were mostly of the R3 type whatever the phylogroup while, within phylogroup B2, strains carrying a K-12 core all belonged to the complex STc131, one of the major clones of extraintestinal pathogenic E. coli (ExPEC) strains. The origin of this uneven distribution is discussed but remains to be fully explained, as well as the consequences of carrying a specific core type on the wider aspects of bacterial phenotype.

scholarly journals Genome-based analyses reveal the presence of 12 heterotypic synonyms in the genus Streptomyces and emended descriptions of Streptomyces bottropensis, Streptomyces celluloflavus, Streptomyces fulvissimus, Streptomyces glaucescens, Streptomyces murinus, and Streptomyces variegatus

2020 ◽  
Vol 70 (6) ◽  
pp. 3924-3929 ◽  
Author(s):  
Munusamy Madhaiyan ◽  
Venkatakrishnan Sivaraj Saravanan ◽  
Wah-Seng See-Too
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Orthologous Gene ◽  
Gene Clusters ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
Genus Streptomyces ◽  
Content Type ◽  
Link Type ◽  
Streptomyces Glaucescens

Phylogenetic analysis based on 16S rRNA gene sequences of the genus Streptomyces showed the presence of six distinguishable clusters, with 100 % sequence similarity values among strains in each cluster; thus they shared almost the same evolutionary distance. This result corroborated well with the outcome of core gene (orthologous gene clusters) based genome phylogeny analysis of 190 genomes including the Streptomyces species in those six clusters. These preeminent results led to an investigation of genome-based indices such as digital DNA–DNA hybridization (dDDH), average nucleotide identity (ANI) and average amino acid identity (AAI) for the strains in those six clusters. Certain strains recorded genomic indices well above the threshold values (70 %, 95–96 % and >95 % for dDDH, ANI and AAI, respectively) determined for species affiliation, suggesting only one type strain belongs to described species and the other(s) may need to be reduced in taxa to a later heterotypic synonym. To conclude, the results of comprehensive analyses based on phylogenetic and genomic indices suggest that the following six reclassifications are proposed: Streptomyces flavovariabilis as a later heterotypic synonym of Streptomyces variegatus ; Streptomyces griseofuscus as a later heterotypic synonym of Streptomyces murinus ; Streptomyces kasugaensis as a later heterotypic synonym of Streptomyces celluloflavus ; Streptomyces luridiscabiei as a later heterotypic synonym of Streptomyces fulvissimus ; Streptomyces pharetrae as a later heterotypic synonym of Streptomyces glaucescens ; and Streptomyces stelliscabiei as a later heterotypic synonym of Streptomyces bottropensis .

scholarly journals Reclassification of the biocontrol agents Bacillus subtilis BY-2 and Tu-100 as Bacillus velezensis and insights into the genomic and specialized metabolite diversity of the species

Microbiology ◽  
2020 ◽  
Vol 166 (12) ◽  
pp. 1121-1128 ◽  
Author(s):  
Alex J. Mullins ◽  
Yinshui Li ◽  
Lu Qin ◽  
Xiaojia Hu ◽  
Lihua Xie ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Natural Product ◽  
Type Species ◽  
Bacterial Species ◽  
Gene Clusters ◽  
Core Gene ◽  
Biocontrol Agents ◽  
Bacillus Velezensis ◽  
Content Type ◽  
Link Type

The genomes of two historical Bacillus species strains isolated from the roots of oilseed rape and used routinely in PR China as biocontrol agents to suppress Sclerotinia disease were sequenced. Average nucleotide identity (ANI) and digital DNA–DNA hybridization analyses demonstrated that they were originally misclassified as Bacillus subtilis and now belong to the bacterial species Bacillus velezensis . A broader ANI analysis of available Bacillus genomes identified 292 B. velezensis genomes that were then subjected to core gene analysis and phylogenomics. Prediction and dereplication of specialized metabolite biosynthetic gene clusters (BGCs) defined the prevalence of multiple antimicrobial-associated BGCs and highlighted the natural product potential of B. velezensis . By defining the core and accessory antimicrobial biosynthetic capacity of the species, we offer an in-depth understanding of B. velezensis natural product capacity to facilitate the selection and testing of B. velezensis strains for use as biological control agents.

Micromonospora humida sp. nov., exhibiting antimicrobial potential, isolated from riverside soil

2021 ◽  
Vol 71 (12) ◽  
Author(s):  
Jun Sik Ra ◽  
Min Ji Kim ◽  
Dong Hyeon Lee ◽  
Ji Won Jeong ◽  
Seung Bum Kim
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Gene Clusters ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Biosynthetic Gene Clusters ◽  
Content Type ◽  
Link Type ◽  
Type Strains ◽  
The 16S Rrna Gene

An actinobacterial strain designated MMS20-R1-14T was isolated from a riverside soil sample. Colonies on agar plates were orange to strong orange brown in colour, which later became black. The cells grew at 10–40 °C (optimum, 37 °C), pH 5.0–11.0 (pH 8.0) and in the presence of 0–4 % NaCl (1 %). The 16S rRNA gene sequence of strain MMS20-R1-14T showed highest similarities to Micromonospora wenchangensis CCTCC AA 2012002T (99.51 %) and Micromonospora rifamycinica AM105T (99.37 %). The orthoANI values between strain MMS20-R1-14T and the two type strains were 95.72 and 90.99 %, and the digital DNA–DNA hybridization values were 63.6 and 40.8 %, respectively, thus confirming the distinction of strain MMS20-R1-14T from its mostly related species. The DNA G+C content of strain MMS20-R1-14T was 72.9 mol%. The strain contained meso-diaminopimelic acid as the major cell-wall amino acid, and the characteristic whole-cell sugars were arabinose, xylose, glucose, ribose and rhamnose. The main cellular fatty acids were C18 : 1  ω9c, iso-C15 : 0 and iso-C16 : 0, the diagnostic polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, and the predominant menaquinones were MK-10(H4) and MK-10(H6), all of which were consistent with those of Micromonospora . Strain MMS20-R1-14T showed antimicrobial activity against a range of bacterial and yeast species. The genome of the strain was found to contain 33 potential biosynthetic gene clusters for secondary metabolites, thus showing a high potential as a producer of bioactive compounds. On the basis of these phenotypic, genotypic and chemotaxonomic data, strain MMS20-R1-14T merits recognition as representing a novel species of the genus Micromonospora , for which the name Micromonospora humida sp. nov. (type strain=MMS20 R1-14T=KCTC 49541T=JCM 34494T) is proposed.

scholarly journals Promoter Swapping Unveils the Role of the Citrobacter rodentium CTS1 Type VI Secretion System in Interbacterial Competition

2012 ◽  
Vol 79 (1) ◽  
pp. 32-38 ◽  
Author(s):  
Erwan Gueguen ◽  
Eric Cascales
Keyword(s):  
Gene Clusters ◽  
Secretion System ◽  
Citrobacter Rodentium ◽  
Type Vi Secretion System ◽  
Content Type ◽  
Type Vi Secretion ◽  
Artificial Induction ◽  
Release Assay ◽  
Promoter Swapping

ABSTRACT The type VI secretion system (T6SS) is a versatile secretion machine dedicated to various functions in Gram-negative bacteria, including virulence toward eukaryotic cells and antibacterial activity. Activity of T6SS might be followed in vitro by the release of two proteins, Hcp and VgrG, in the culture supernatant. Citrobacter rodentium , a rodent pathogen, harbors two T6SS gene clusters, cts1 and cts2 . Reporter fusion and Hcp release assays suggested that the CTS1 T6SS was not produced or not active. The cts1 locus is composed of two divergent operons. We therefore developed a new vector allowing us to swap the two divergent endogenous promoters by P tac and P BAD using the λ red recombination technology. Artificial induction of both promoters demonstrated that the CTS1 T6SS is functional as shown by the Hcp release assay and confers on C. rodentium a growth advantage in antibacterial competition experiments with Escherichia coli .

scholarly journals Glycomyces terrestris sp. nov., isolated from extremely arid soil from Yuanmou Earth Forest

2020 ◽  
Author(s):  
Qinyuan Li ◽  
Guiding Li ◽  
Lei Lang ◽  
Defeng An ◽  
Chenglin Jiang ◽  
...  
Keyword(s):  
Type Species ◽  
Draft Genome ◽  
Gene Clusters ◽  
Major Fatty Acid ◽  
Closely Related Species ◽  
Content Type ◽  
Arid Soil ◽  
Link Type ◽  
Pr China ◽  
Fatty Acid Compositions

A Gram-stain-positive, mycelium-forming actinobacterium, YIM 121974T was isolated from an extreme arid soil sample collected at Yuanmou Earth Forest, Yunnan Province, PR China. Classification using a polyphasic approach suggested that strain YIM 121974T belonged to the genus Glycomyces and was closely related to Glycomyces dulcitolivorans SJ-25T (98.3 %), Glycomyces scopariae YIM 56256T (98 %), Glycomyces mayteni YIM 61331T (97.9 %), Glycomyces albidus NEAU-7082T (97.9 %), Glycomyces sambucus CGMCC 4.3147T (97.7 %), Glycomyces artemisiae IXS4T (97.6 %) and Glycomyces parisis CPCC 204357T (97.5 %), but could be distinguished from its closest relatives by a combination of phenotypic and phylogenetic features. Average nucleotide identity values of YIM 121974T to its closest phylogenetic neighbours were 70.7–88.9 %, which are lower than the threshold of 95 %. The digital DNA–DNA hybridization values between YIM 121974T and these relative species were 18.0–36.3 %, which are also well below the cut-off value (>70 %) for species delineation. The DNA G+C content of strain YIM 121974T was 72.3 mol% (draft genome sequence). The predominant menaquinone was MK-11. The phospholipids were composed of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, phosphoglycolipid and glycolipid. The major fatty acid compositions were iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. The draft genome of isolate YIM 121974T was found to contain 11 secondary metabolite biosynthesis gene clusters by using the antiSMASH server. Based on the above observations, strain YIM 121974T could be distinguished from closely related species belonging to the genus Glycomyces . Thus, strain YIM 121974T represents a novel species of the genus Glycomyces , for which the name Glycomyces terrestris sp. nov. is proposed. The type strain is YIM 121974T (=KCTC 39870T=DSM 106742T).

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