New insights in Tibial muscular dystrophy revealed by protein-protein interaction networks

Leite, Giuseppe Gianini Figueirêdo; Blighe, Kevin

doi:10.1101/271411

Cited by 2 publications

(2 citation statements)

References 71 publications

(66 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…To assess sample reproducibility, PCA and MA plots were generated using DESeq2's plotPCA and plotMA functions. Volcano plots for each strain were made using EnhancedVolcano (74). The PCA on the expression of all orthogroups in the core genome across all strains was based on a matrix with a single average Log 2 FC value for all genes within an orthogroup.…”

Section: Differential Expression Analyses Of the Rna-seq Resultsmentioning

confidence: 99%

Comparative transcriptomics reveal a highly polymorphicXanthomonasHrpG virulence regulon

Quiroz Monnens,

Roux,

Cunnac

et al. 2024

Preprint

View full text Add to dashboard Cite

Bacteria of the genusXanthomonascause economically significant diseases in various crops. Their virulence is dependent on the translocation of type III effectors (T3Es) into plant cells by the type III secretion system (T3SS), a process regulated by the master response regulator HrpG. Although HrpG has been studied for over two decades, its regulon across diverseXanthomonasspecies, particularly beyond type III secretion, remains understudied. In this study, we conducted transcriptome sequencing to explore the HrpG regulons of 17Xanthomonasstrains, encompassing six species and nine pathovars, each exhibiting distinct host and tissue specificities. We employed constitutive expression of plasmid-bornehrpG*, which encodes a constitutively active form of HrpG, to induce the regulon. Our findings reveal substantial inter- and intra-specific diversity in the HrpG* regulons across the strains. Besides 21 genes directly involved in the biosynthesis of the T3SS, the core HrpG* regulon is limited to only five additional genes encoding the transcriptional activator HrpX, the two T3E proteins XopR and XopL, a major facility superfamily (MFS) transporter, and the phosphatase PhoC. Interestingly, genes involved in chemotaxis and genes encoding enzymes with carbohydrate-active and proteolytic activities are variably regulated by HrpG*. The diversity in the HrpG* regulon suggests that HrpG-dependent virulence inXanthomonasmight be achieved through several distinct strain-specific strategies, potentially reflecting adaptation to diverse ecological niches. These findings enhance our understanding of the complex role of HrpG in regulating various virulence and adaptive pathways, extending beyond T3Es and the T3SS.

show abstract

Section: Differential Expression Analyses Of the Rna-seq Resultsmentioning

confidence: 99%

Comparative transcriptomics reveal a highly polymorphicXanthomonasHrpG virulence regulon

Quiroz Monnens,

Roux,

Cunnac

et al. 2024

Preprint

View full text Add to dashboard Cite

show abstract

“…To create a model mean-variance trend and fit the linear model to the data, the voom function from the Bioconductor/R package limma (56) was used to model a mean-variance relationship, the function lmfit was used to fit a linear model to the data, and makeContrasts was used to make contrasts of the design matrix between the 2'-FL group versus the Glc group. The R package EnhancedVolcano was used to generate volcano plots highlighting the GH29 and GH95 genes for each Akkermansia strain with strict cutoff values (p ≤0.05, log2 fold change ≥ 2) (58).…”

Section: Rna Sequencing and Analysismentioning

confidence: 99%

Mechanism of 2’-Fucosyllactose degradation by Human-AssociatedAkkermansia

Padilla,

Fricker,

Luna

et al. 2023

Preprint

View full text Add to dashboard Cite

Among the first microorganisms to colonize the human gut of breastfed infants are bacteria capable of fermenting human milk oligosaccharides (HMOs). One of the most abundant HMOs, 2’-fucosyllactose (2’-FL), may specifically drive bacterial colonization of the intestine. Recently, differential growth has been observed across multiple species of Akkermansia on various HMOs including 2’FL. In culture, we found growth of two species, A. muciniphila MucTand A. biwaensis CSUN-19, in HMOS corresponded to a decrease in the levels of 2’-FL and an increase in lactose, indicating that the first step in 2’-FL catabolism is the cleavage of fucose. Using phylogenetic analysis and transcriptional profiling, we found that the number and expression of fucosidase genes from two glycoside hydrolase (GH) families, GH29 and GH95, varies between these two species. During mid-log phase growth, the expression of several GH29 genes was increased by 2’-FL in both species, whereas the GH95 genes were induced only in A. muciniphila. We further show that one putative fucosidase and a β-galactosidase from A. biwaensis are involved in the breakdown of 2’-FL. Our findings indicate that that plasticity of GHs of human associated Akkermansia sp. enable access to additional growth substrates present in HMOs, including 2’-FL. Our work highlights the potential for Akkermansia to influence the development of the gut microbiota early in life and expands the known metabolic capabilities of this important human symbiont.

show abstract

New insights in Tibial muscular dystrophy revealed by protein-protein interaction networks

Cited by 2 publications

References 71 publications

Comparative transcriptomics reveal a highly polymorphicXanthomonasHrpG virulence regulon

Comparative transcriptomics reveal a highly polymorphicXanthomonasHrpG virulence regulon

Mechanism of 2’-Fucosyllactose degradation by Human-AssociatedAkkermansia

Contact Info

Product

Resources

About