KAAS: an automatic genome annotation and pathway reconstruction server

Moriya, Yuki; Itoh, Masumi; Okuda, Shujiro; Yoshizawa, Akiyasu C.; Kanehisa, Minoru

doi:10.1093/nar/gkm321

Cited by 3,409 publications

(2,484 citation statements)

References 10 publications

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“…Genes were assigned to Clusters of Orthologous Groups (COGs) as follows. A. actinomycetemcomitans VT1169 and 624 were first annotated with K numbers as described previously (33) using the KEGG Automatic Annotation Server (KAAS) (95). K numbers were then converted to COGs (49) using the binary relationship file provided on the KEGG website (http://www .genome.jp/kegg/files/ko2cog.xl).…”

Section: Methodsmentioning

confidence: 99%

“…The KEGG application programming interface (API) first was used to find (i) the list of R numbers associated with each K number (http://rest.kegg.jp/link/rn/ko) and (ii) the list of C numbers associated with each R number (http://rest.kegg.jp/link/cpd/rn) in the KEGG database. These lists were then used with the countif function in Microsoft Excel to find the list of C numbers (via the R numbers) associated with each K number in the A. actinomycetemcomitans VT1169 and 624 genomes (obtained using KAAS [95]). The KEGG Mapper Search and Color Pathway tool was then used to generate a metabolic map for the combined list of A. actinomycetemcomitans K and C numbers, both of which were colored black.…”

Section: Methodsmentioning

confidence: 99%

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Defining Genetic Fitness Determinants and Creating Genomic Resources for an Oral Pathogen

Narayanan

Ramsey

Stacy

et al. 2017

Appl Environ Microbiol

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Periodontitis is a microbial infection that destroys the structures that support the teeth. Although it is typically a chronic condition, rapidly progressing, aggressive forms are associated with the oral pathogen Aggregatibacter actinomycetemcomitans. One of this bacterium's key virulence traits is its ability to attach to surfaces and form robust biofilms that resist killing by the host and antibiotics. Though much has been learned about A. actinomycetemcomitans since its initial discovery, we lack insight into a fundamental aspect of its basic biology, as we do not know the full set of genes that it requires for viability (the essential genome). Furthermore, research on A. actinomycetemcomitans is hampered by the field's lack of a mutant collection. To address these gaps, we used rapid transposon mutant sequencing (Tn-seq) to define the essential genomes of two strains of A. actinomycetemcomitans, revealing a core set of 319 genes. We then generated an arrayed mutant library comprising Ͼ1,500 unique insertions and used a sequencing-based approach to define each mutant's position (well and plate) in the library. To demonstrate its utility, we screened the library for mutants with weakened resistance to subinhibitory erythromycin, revealing the multidrug efflux pump AcrAB as a critical resistance factor. During the screen, we discovered that erythromycin induces A. actinomycetemcomitans to form biofilms. We therefore devised a novel Tnseq-based screen to identify specific factors that mediate this phenotype and in follow-up experiments confirmed 4 mutants. Together, these studies present new insights and resources for investigating the basic biology and disease mechanisms of a human pathogen. IMPORTANCE Millions suffer from gum disease, which often is caused by Aggregatibacter actinomycetemcomitans, a bacterium that forms antibiotic-resistant biofilms. To fully understand any organism, we should be able to answer: what genes does it require for life? Here, we address this question for A. actinomycetemcomitans by determining the genes in its genome that cannot be mutated. As for the genes that can be mutated, we archived these mutants into a library, which we used to find genes that contribute to antibiotic resistance, leading us to discover that antibiotics cause A. actinomycetemcomitans to form biofilms. We then devised an approach to find genes that mediate this process and confirmed 4 genes. These results illuminate new fundamental traits of a human pathogen.KEYWORDS Aggregatibacter, Tn-seq, antibiotics, biofilms, essential genome O ne of the longest-studied human microbiomes is the "animalcules" (bacteria), first observed by van Leeuwenhoek (1), that inhabit the oral cavity. Oral bacteria readily attach to tooth surfaces and develop into spatially organized, multispecies biofilms (2). These communities also persist beneath the gum line in the subgingival pocket, where they are kept in check by host immune cells (3). Though normally benign, subgingival communities can accumulate opportunistic oral p...

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Defining Genetic Fitness Determinants and Creating Genomic Resources for an Oral Pathogen

Narayanan

Ramsey

Stacy

et al. 2017

Appl Environ Microbiol

View full text Add to dashboard Cite

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“…Additionally, a GO enrichment analysis using Fisher's exact test was also performed in Blast2GO to test whether any of the GO terms appeared significantly over‐ or underrepresented in a pairwise comparison between the two ontogenetic stages. Finally, a comparison of overall nucleotide sequence homology between the gastrula and pluteus transcriptome of M. franciscanus and the genome of S. purpuratus was completed using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and its automated assignment server (KAAS; Moriya, Itoh, Okuda, Yoshizawa, & Kanehisa, 2007). …”

Section: Methodsmentioning

confidence: 99%

Gene expression profiling during the embryo‐to‐larva transition in the giant red sea urchin Mesocentrotus franciscanus

Gaitán‐Espitía

Hofmann

2017

Ecology and Evolution

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In echinoderms, major morphological transitions during early development are attributed to different genetic interactions and changes in global expression patterns that shape the regulatory program for the specification of embryonic territories. In order more thoroughly to understand these biological and molecular processes, we examined the transcriptome structure and expression profiles during the embryo‐to‐larva transition of a keystone species, the giant red sea urchin Mesocentrotus franciscanus. Using a de novo assembly approach, we obtained 176,885 transcripts from which 60,439 (34%) had significant alignments to known proteins. From these transcripts, ~80% were functionally annotated allowing the identification of ~2,600 functional, structural, and regulatory genes involved in developmental process. Analysis of expression profiles between gastrula and pluteus stages of M. franciscanus revealed 791 differentially expressed genes with 251 GO overrepresented terms. For gastrula, up‐regulated GO terms were mainly linked to cell differentiation and signal transduction involved in cell cycle checkpoints. In the pluteus stage, major GO terms were associated with phosphoprotein phosphatase activity, muscle contraction, and olfactory behavior, among others. Our evolutionary comparative analysis revealed that several of these genes and functional pathways are highly conserved among echinoids, holothuroids, and ophiuroids.

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“…InterPro terms were also obtained from InterProScan at EBI, converted and merged with GOs using Blast2GO software. Finally, the KEGG (Kyoto Encyclopedia of Genes and Genome) orthology (KO) identifiers, or the K numbers, were generated using the web-based server KAAS (KEGG Automatic Annotation Server) (Moriya et al, 2007), resulting in the mapping of putative KEGG metabolic pathways of C. brasiliana. The transcripts assigned to each gene family were first identified based on the closest blastx matches in the NCBI nr database, followed by the identification of at least one of the descriptors provided by the relevant InterPro Scan and Pfam domain (Supplementary Table S2).…”

Section: Functional Annotation and Mappingmentioning

confidence: 99%

Key metabolic pathways involved in xenobiotic biotransformation and stress responses revealed by transcriptomics of the mangrove oyster Crassostrea brasiliana

et al. 2015

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Key metabolic pathways involved in xenobiotic biotransformation and stress responses revealed by transcriptomics of the mangrove oyster Crassostrea brasiliana.Aquatic Toxicology http://dx.doi.org/10. 1016/j.aquatox.2015.06.012 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. Highlights-Thetranscriptome of the mangrove oyster Crassostrea brasilianawas sequenced.-The sequencing effort dramatically expanded the existing cDNA sequences available for the species.-Global analysis for transcription in the oyster treated with phenanthrene, diesel and domestic sewage was performed.-The pollutants altered mRNAs for genes in biotransformation, antioxidant and stress response pathways. Abstract 2The Brazilian oyster Crassostrea brasiliana was challenged to three common environmental contaminants: phenanthrene, diesel fuel water-accommodated fraction (WAF) and domestic sewage. Total RNA was extracted from the gill and digestive gland, and cDNA libraries were sequenced using the 454 FLX pla orm. The assembled transcriptome resulted in ˜20,000contigs, which were annotated to produce the first de novo transcriptome for C. brasiliana.Sequences were screened to identify genes potentially involved in the biotransformation of xenobiotics and associated antioxidant defence mechanisms. These gene families included those of the cytochrome P450 (CYP450), 70kDa heat shock, antioxidants, such as glutathione Stransferase, superoxide dismutase, catalase and also multi-drug resistance proteins. Analysis showed that the massive expansion of the CYP450 and HSP70 family due to gene duplication identified in the Crassostrea gigas genome also occurred in C. brasiliana, suggesting these processes form the base of the Crassostrea lineage. Preliminary expression analyses revealed several candidates biomarker genes that were up-regulated during each of the three treatments, suggesting the potential for environmental monitoring.

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KAAS: an automatic genome annotation and pathway reconstruction server

Cited by 3,409 publications

References 10 publications

Defining Genetic Fitness Determinants and Creating Genomic Resources for an Oral Pathogen

Defining Genetic Fitness Determinants and Creating Genomic Resources for an Oral Pathogen

Gene expression profiling during the embryo‐to‐larva transition in the giant red sea urchin Mesocentrotus franciscanus

Key metabolic pathways involved in xenobiotic biotransformation and stress responses revealed by transcriptomics of the mangrove oyster Crassostrea brasiliana

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