MicrobesOnline: an integrated portal for comparative and functional genomics

Bacterial pathogens can exploit metabolic pathways to facilitate their successful infection cycles, but little is known about roles of d‐galactosamine (GalN)/N‐acetyl‐d‐galactosamine (GalNAc) catabolism pathway in bacterial pathogenesis. Here, we report the genomic reconstruction of GalN/GalNAc utilization pathway in Streptococci and the diversified aga regulons. We delineated two new paralogous AgaR regulators for the GalN/GalNAc catabolism pathway. The electrophoretic mobility shift assays experiment demonstrated that AgaR2 (AgaR1) binds the predicted palindromes, and the combined in vivo data from reverse transcription quantitative polymerase chain reaction and RNA‐seq suggested that AgaR2 (not AgaR1) can effectively repress the transcription of the target genes. Removal of agaR2 (not agaR1) from Streptococcus suis 05ZYH33 augments significantly the abilities of both adherence to Hep‐2 cells and anti‐phagocytosis against RAW264.7 macrophage. As anticipated, the dysfunction in AgaR2‐mediated regulation of S. suis impairs its pathogenicity in experimental models of both mice and piglets. Our finding discovered two novel regulators specific for GalN/GalNAc catabolism and assigned them distinct roles into bacterial infections. To the best of our knowledge, it might represent a first paradigm that links the GalN/GalNAc catabolism pathway to bacterial pathogenesis.

show abstract

“…2010). Identification of orthologs was performed using the BLASTP search in the non‐redundant database (Altschul et al.…”

Section: Methodsmentioning

confidence: 99%

Two novel regulators of N‐acetyl‐galactosamine utilization pathway and distinct roles in bacterial infections

Zhang

Ravcheev

et al. 2015

MicrobiologyOpen

View full text Add to dashboard Cite

show abstract

“…Protein sequences of crp homologues were imported into MEGA 5 software (Tamura et al, 2011) from MicrobesOnline (Dehal et al, 2010) and the Comprehensive Microbial Resource (Peterson et al, 2001). Evolutionary history was reconstructed using the neighbour-joining method with a bootstrap test (1000 replicates) to determine the percentage of replicate trees in which the associated taxa clustered together.…”

Section: Methodsmentioning

confidence: 99%

Novel regulatory roles of cAMP receptor proteins in fast-growing environmental mycobacteria

et al. 2015

View full text Add to dashboard Cite

Mycobacterium smegmatis is a fast-growing, saprophytic, mycobacterial species that contains two cAMP-receptor protein (CRP) homologues designated herein as Crp1 and Crp2. Phylogenetic analysis suggests that Crp1 (Msmeg_0539) is uniquely present in fast-growing environmental mycobacteria, whereas Crp2 (Msmeg_6189) occurs in both fast-and slowgrowing species. A crp1 mutant of M. smegmatis was readily obtained, but crp2 could not be deleted, suggesting it was essential for growth. A total of 239 genes were differentially regulated in response to crp1 deletion (loss of function), including genes coding for mycobacterial energy generation, solute transport and catabolism of carbon sources. To assess the role of Crp2 in M. smegmatis, the crp2 gene was overexpressed (gain of function) and transcriptional profiling studies revealed that 58 genes were differentially regulated. Identification of the CRP promoter consensus in M. smegmatis showed that both Crp1 and Crp2 recognized the same consensus sequence (TGTGN 8 CACA). Comparison of the Crp1-and Crp2-regulated genes revealed distinct but overlapping regulons with 11 genes in common, including those of the succinate dehydrogenase operon (MSMEG_0417-0420, sdh1). Expression of the sdh1 operon was negatively regulated by Crp1 and positively regulated by Crp2. Electrophoretic mobility shift assays with purified Crp1 and Crp2 demonstrated that Crp1 binding to the sdh1 promoter was cAMP-independent whereas Crp2 binding was cAMP-dependent. These data suggest that Crp1 and Crp2 respond to distinct signalling pathways in M. smegmatis to coordinate gene expression in response to carbon and energy supply.

show abstract

“…These include stand-alone software such as MEGAN [6], HUMAnN [7], RAMMCAP [8], SmashCommunity [9], and MOCAT [10], as well as cloud-based tools like CloVR [11], and web portals like MG-RAST [12], MicrobesOnline [13], and the IMG/M annotation server [14](S1 Table). Generally, these methods operate by comparing metagenomic sequence reads to a reference database of functionally annotated protein families and use homology inference to annotate each read [5].…”

Section: Introductionmentioning

confidence: 99%

Automated and accurate estimation of gene family abundance from shotgun metagenomes

Nayfach

Bradley

Wyman

et al. 2015

Preprint

View full text Add to dashboard Cite

Shotgun metagenomic DNA sequencing is a widely applicable tool for characterizing the functions that are encoded by microbial communities. Several bioinformatic tools can be used to functionally annotate metagenomes, allowing researchers to draw inferences about the functional potential of the community and to identify putative functional biomarkers. However, little is known about how decisions made during annotation affect the reliability of the results. Here, we use statistical simulations to rigorously assess how to optimize annotation accuracy and speed, given parameters of the input data like read length and library size. We identify best practices in metagenome annotation and use them to guide the development of the Shotgun Metagenome Annotation Pipeline (ShotMAP). ShotMAP is an analytically flexible, end-to-end annotation pipeline that can be implemented either on a local computer or a cloud compute cluster. We use ShotMAP to assess how different annotation databases impact the interpretation of how marine metagenome and metatranscriptome functional capacity changes across seasons. We also apply ShotMAP to data obtained from a clinical microbiome investigation of inflammatory bowel disease. This analysis finds that gut microbiota collected from Crohn's disease patients are functionally distinct from gut microbiota collected from either ulcerative colitis patients or healthy controls, with differential abundance of metabolic pathways related to host-microbiome interactions that may serve as putative biomarkers of disease. Author SummaryMicrobial communities perform a wide variety of functions, from marine photosynthesis to aiding digestion in the human gut. Shotgun "metagenomic" sequencing can be used to sample millions of short DNA sequences from such communities directly, without needing to first culture its constituents in the laboratory. Using these data, researchers can survey which functions are encoded by mapping these short sequences to known protein families and pathways. Several tools for this annotation already exist. But, annotation is a multi-step process that includes identification of genes in a metagenome and determination of the type of protein each gene encodes. We currently know little about how different choices of parameters during annotation influences the final results. In this work, we systematically test how several key decisions affect the accuracy and speed of annotation, and based on these results, develop new software for annotation, which we named ShotMAP. We then use ShotMAP to functionally characterize marine communities and gut communities in a clinical cohort of inflammatory bowel disease. We find several functions are differentially represented in the gut microbiome of Crohn's disease patients, which could be candidates for biomarkers and could also offer insight into the pathophysiology of Crohn's. ShotMAP is freely available (https://github.com/sharpton/shotmap).

show abstract

MicrobesOnline: an integrated portal for comparative and functional genomics

Cited by 415 publications

References 27 publications

Two novel regulators of N‐acetyl‐galactosamine utilization pathway and distinct roles in bacterial infections

Two novel regulators of N‐acetyl‐galactosamine utilization pathway and distinct roles in bacterial infections

Novel regulatory roles of cAMP receptor proteins in fast-growing environmental mycobacteria

Automated and accurate estimation of gene family abundance from shotgun metagenomes

Contact Info

Product

Resources

About