Improving the consistency of domain annotation within the Conserved Domain Database

Derbyshire, Myra K.; Gonzales, Noreen R.; Lu, Shuo; He, Jane; Marchler, Gabriele H.; Wang, Zhouxi; Marchler‐Bauer, Aron

doi:10.1093/database/bav012

Cited by 19 publications

(14 citation statements)

References 12 publications

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“…Candidate sequences were aligned using ClustalX2 and a neighbor-joining phylogram was constructed, with both using the default parameters. The NCBI Conserved Domain Search tool was used to examine the sequences for conserved regions against the Conserved Domains Database, v3.13 (Derbyshire et al, 2015 ).…”

Section: Methodsmentioning

confidence: 99%

Metabolic Consequences of Infection of Grapevine (Vitis vinifera L.) cv. “Modra frankinja” with Flavescence Dorée Phytoplasma

et al. 2016

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Flavescence dorée, caused by the quarantine phytoplasma FDp, represents the most devastating of the grapevine yellows diseases in Europe. In an integrated study we have explored the FDp–grapevine interaction in infected grapevines of cv. “Modra frankinja” under natural conditions in the vineyard. In FDp-infected leaf vein-enriched tissues, the seasonal transcriptional profiles of 14 genes selected from various metabolic pathways showed an FDp-specific plant response compared to other grapevine yellows and uncovered a new association of the SWEET17a vacuolar transporter of fructose with pathogens. Non-targeted metabolome analysis from leaf vein-enriched tissues identified 22 significantly changed compounds with increased levels during infection. Several metabolites corroborated the gene expression study. Detailed investigation of the dynamics of carbohydrate metabolism revealed significant accumulation of sucrose and starch in the mesophyll of FDp-infected leaves, as well as significant up-regulation of genes involved in their biosynthesis. In addition, infected leaves had high activities of ADP-glucose pyrophosphorylase and, more significantly, sucrose synthase. The data support the conclusion that FDp infection inhibits phloem transport, resulting in accumulation of carbohydrates and secondary metabolites that provoke a source-sink transition and defense response status.

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Section: Methodsmentioning

confidence: 99%

Metabolic Consequences of Infection of Grapevine (Vitis vinifera L.) cv. “Modra frankinja” with Flavescence Dorée Phytoplasma

et al. 2016

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“… A. Schematic of the BB0794 protein. The gray boxes from amino acids 1–34 indicate the putative N-terminal signal peptide predicted by PrediSi ( Nielsen et al ., 1997 ) while amino acid 1117–1443 represent the C-terminal DUF490 domain identified by the Conserved Domain Database (CDD) algorithm ( Derbyshire et al ., 2015 ). …”

Section: Figmentioning

confidence: 99%

The TamB ortholog of Borrelia burgdorferi interacts with the β‐barrel assembly machine (BAM) complex protein BamA

Iqbal

Kenedy

Lybecker

et al. 2016

Molecular Microbiology

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Summary Two outer membrane protein (OMP) transport systems in diderm bacteria assist in assembly and export of OMPs. These two systems are the β-barrel assembly machine (BAM) complex and the translocation and assembly module (TAM). The BAM complex consists of the OMP component BamA along with several outer membrane associated proteins. The TAM also consists of an OMP, designated TamA, and a single inner membrane (IM) protein, TamB. Together TamA and TamB aid in the secretion of virulence-associated OMPs. In this study we characterized the hypothetical protein BB0794 in Borrelia burgdorferi. BB0794 contains a conserved DUF490 domain, which is a motif found in all TamB proteins. All spirochetes lack a TamA ortholog, but computational and physicochemical characterization of BB0794 revealed it is a TamB ortholog. Interestingly, BB0794 was observed to interact with BamA and a BB0794 regulatable mutant displayed altered cellular morphology and antibiotic sensitivity. The observation that B. burgdorferi contains a TamB ortholog that interacts with BamA and is required for proper outer membrane biogenesis not only identifies a novel role for TamB-like proteins, but also may explain why most diderms harbor a TamB-like protein while only a select group encodes TamA.

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“…Additional clusters were included in the analyzed set based on the phylogenetic representation of their members. Selected representatives of each cluster were checked for the presence of known protein domains in their N-terminal regions using CD-Search (70) with relaxed parameters (expect value cut-off of 10) and the predicted structural similarity to PilZ was checked using HHPred (64, 65). Protein secondary structures were taken from the HHpred outputs or predicted using JPred (71).…”

Section: Methodsmentioning

confidence: 99%

Structural conservation and diversity of PilZ-related domains

Galperin

Chou

2019

Preprint

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The widespread bacterial second messenger cyclic diguanylate (c-di-GMP) regulates a 1 variety of processes, including protein secretion, motility, cell development, and biofilm 2 formation. C-di-GMP-dependent responses are often mediated by its binding to the 3 cytoplasmic receptors that contain the PilZ domain. We present here comparative 4 structural and sequence analysis of various PilZ-related domains and describe three 5 principal types of them: (i) the canonical PilZ domain, whose structure includes a six-6 stranded beta-barrel and a C-terminal alpha-helix; (ii) an atypical PilZ domain that 7 contains two extra alpha-helices and forms stable tetramers, and (iii) divergent PilZ-8 related domains, which include the eponymous PilZ protein and PilZN (YcgR_N) and 9 PilZNR (YcgR_2) domains. We refine the second c-di-GMP binding motif of PilZ as 10 [D/N]hSxxG and show that the hydrophobic residue h of this motif interacts with a cluster 11 of conserved hydrophobic residues, helping maintain the PilZ domain fold. We describe 12 several novel PilZN-type domains that are fused to the canonical PilZ domains in specific 13 taxa, such as spirochetes, actinobacteria, cellulosolytic clostridia, deltaproteobacteria, 14 and aquificae. We propose that the evolution of three major groups of PilZ domains 15 included (i) fusion of pilZ with other genes, which produced Alg44, cellulose synthase, and 16 other multidomain proteins; (ii) insertion of a ~200-bp fragment, which resulted in the 17 formation of tetramer-forming PilZ proteins, and (iii) tandem duplication of pilZ genes, 18 which led to the formation of PilZ dimers and YcgR-like proteins. 19 IMPORTANCE 20Cyclic di-GMP is a ubiquitous bacterial second messenger that regulates motility, biofilm 21 formation and virulence of many bacterial pathogens. The PilZ domain is a widespread c-22 di-GMP receptor that binds c-di-GMP through its RxxxR and [D/N]xSxxG motifs; some PilZ 23 domains lack these motifs and are unable to bind c-di-GMP. We used structural and 24 sequence analysis to assess the diversity of PilZ-related domains and define their common 25 features. We show that the hydrophobic residue h in the second motif is highly conserved; 26 it may serve as a readout for c-di-GMP binding. We describe three principal classes of 27 PilZ-related domains: canonical, tetramer-forming, and divergent PilZ domains, and 28 propose the evolutionary pathways that led to the emergence of these PilZ types. 29 30

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Improving the consistency of domain annotation within the Conserved Domain Database

Cited by 19 publications

References 12 publications

Metabolic Consequences of Infection of Grapevine (Vitis vinifera L.) cv. “Modra frankinja” with Flavescence Dorée Phytoplasma

Metabolic Consequences of Infection of Grapevine (Vitis vinifera L.) cv. “Modra frankinja” with Flavescence Dorée Phytoplasma

The TamB ortholog of Borrelia burgdorferi interacts with the β‐barrel assembly machine (BAM) complex protein BamA

Structural conservation and diversity of PilZ-related domains

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