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A conserved gene family encodes transmembrane proteins with fibronectin, immunoglobulin and leucine-rich repeat domains (FIGLER)

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BMC BIOLOGY 2007年第1期5卷 36-36页

作者： Munfus, Delicia L. Haga, Christopher L. Burrows, Peter D. Cooper, Max D. Univ Alabama Birmingham Div Dev & Clin Immunol Birmingham AL 35294 USA Univ Alabama Birmingham Dept Microbiol Birmingham AL 35294 USA Univ Alabama Birmingham Dept Genet Birmingham AL 35294 USA Univ Alabama Birmingham Dept Med Birmingham AL 35294 USA Univ Alabama Birmingham Dept Pediat Birmingham AL 35294 USA

Background: In mouse the cytokine interleukin-7 (IL-7) is required for generation of B lymphocytes, but human IL-7 does not appear to have this function. A bioinformatics approach was therefore used to identify IL-7 receptor related genes in the hope of identifying the elusive human cytokine. Results: Our database search identified a family of nine gene candidates, which we have provisionally named fibronectin immunoglobulin leucine-rich repeat (FIGLER). The FIGLER 1-9 genes are predicted to encode type I transmembrane glycoproteins with 6-12 leucine-rich repeats (LRR), a C2 type Ig domain, a fibronectin type III domain, a hydrophobic transmembrane domain, and a cytoplasmic domain containing one to four tyrosine residues. Members of this multichromosomal gene family possess 20-47% overall amino acid identity and are differentially expressed in cell lines and primary hematopoietic lineage cells. Genes for FIGLER homologs were identified in macaque, orangutan, chimpanzee, mouse, rat, dog, chicken, toad, and puffer fish databases. The non-human FIGLER homologs share 38-99% overall amino acid identity with their human counterpart. Conclusion: The extracellular domain structure and absence of recognizable cytoplasmic signaling motifs in members of the highly conserved FIGLER gene family suggest a trophic or cell adhesion function for these molecules.

关键词： basic local alignment search tool Predicted Amino Acid Sequence Simple Modular Architecture Research tool Hydrophobic Transmembrane Domain FNIII Domain

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Medicago truncatula transporter database: a comprehensive database resource for M. truncatula transporters

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BMC GENOMICS 2012年第1期13卷 60-60页

作者： Miao, Zhenyan Li, Daofeng Zhang, Zhenhai Dong, Jiangli Su, Zhen Wang, Tao China Agr Univ Coll Biol Sci State Key Lab Plant Physiol & Biochem Beijing 100193 Peoples R China China Agr Univ Coll Biol Sci State Key Lab Agrobiotechnol Beijing 100193 Peoples R China

Background: Medicago truncatula has been chosen as a model species for genomic studies. It is closely related to an important legume, alfalfa. Transporters are a large group of membrane-spanning proteins. They deliver essential nutrients, eject waste products, and assist the cell in sensing environmental conditions by forming a complex system of pumps and channels. Although studies have effectively characterized individual M. truncatula transporters in several databases, until now there has been no available systematic database that includes all transporters in M. truncatula. Description: The M. truncatula transporter database (MTDB) contains comprehensive information on the transporters in M. truncatula. Based on the TransportTP method, we have presented a novel prediction pipeline. A total of 3,665 putative transporters have been annotated based on International Medicago Genome Annotated Group (IMGAG) V3.5 V3 and the M. truncatula Gene Index (MTGI) V10.0 releases and assigned to 162 families according to the transporter classification system. These families were further classified into seven types according to their transport mode and energy coupling mechanism. Extensive annotations referring to each protein were generated, including basic protein function, expressed sequence tag (EST) mapping, genome locus, three-dimensional template prediction, transmembrane segment, and domain annotation. A chromosome distribution map and text-based basic local alignment search tools were also created. In addition, we have provided a way to explore the expression of putative M. truncatula transporter genes under stress treatments. Conclusions: In summary, the MTDB enables the exploration and comparative analysis of putative transporters in M. truncatula. A user-friendly web interface and regular updates make MTDB valuable to researchers in related fields. The MTDB is freely available now to all users at http://***/MtTransporter/.

关键词： Protein Data Bank Transporter Gene basic local alignment search tool basic local alignment search tool search Tentative Consensus

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BLAST-EXPLORER helps you building datasets for phylogenetic analysis

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BMC EVOLUTIONARY BIOLOGY 2010年第1期10卷 8-8页

作者： Dereeper, Alexis Audic, Stephane Claverie, Jean-Michel Blanc, Guillaume Informat Genom & Struct CNRS Inst Microbiol Mediterranee IFR 88 UPR2589 F-13009 Marseille France

Background: The right sampling of homologous sequences for phylogenetic or molecular evolution analyses is a crucial step, the quality of which can have a significant impact on the final interpretation of the study. There is no single way for constructing datasets suitable for phylogenetic analysis, because this task intimately depends on the scientific question we want to address, Moreover, database mining softwares such as BLAST which are routinely used for searching homologous sequences are not specifically optimized for this task. Results: To fill this gap, we designed BLAST-Explorer, an original and friendly web-based application that combines a BLAST search with a suite of tools that allows interactive, phylogenetic-oriented exploration of the BLAST results and flexible selection of homologous sequences among the BLAST hits. Once the selection of the BLAST hits is done using BLAST-Explorer, the corresponding sequence can be imported locally for external analysis or passed to the phylogenetic tree reconstruction pipelines available on the *** platform. Conclusions: BLAST-Explorer provides a simple, intuitive and interactive graphical representation of the BLAST results and allows selection and retrieving of the BLAST hit sequences based a wide range of criterions. Although BLAST-Explorer primarily aims at helping the construction of sequence datasets for further phylogenetic study, it can also be used as a standard BLAST server with enriched output. BLAST-Explorer is available at http://***

关键词： Query Sequence basic local alignment search tool Sequence Selection basic local alignment search tool search Blast Output

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Characterization of the bovine type I IFN locus: rearrangements, expansions, and novel subfamilies

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BMC GENOMICS 2009年第1期10卷 187-187页

作者： Walker, Angela M. Roberts, R. Michael Univ Missouri Dept Anim Sci Columbia MO 65211 USA Univ Missouri Dept Vet Pathobiol Columbia MO 65211 USA Univ Missouri Christopher S Bond Life Sci Ctr Columbia MO 65211 USA

Background: The Type I interferons (IFN) have major roles in the innate immune response to viruses, a function that is believed to have led to expansion in the number and complexity of their genes, although these genes have remained confined to single chromosomal region in all mammals so far examined. IFNB and IFNE define the limits of the locus, with all other Type I IFN genes except IFNK distributed between these boundaries, strongly suggesting that the locus has broadened as IFN genes duplicated and then evolved into a series of distinct families. Results: The Type I IFN locus in Bos taurus has undergone significant rearrangement and expansion compared to mouse and human, however, with the constituent genes separated into two sub-loci separated by > 700 kb. The IFNW family is greatly expanded, comprising 24 potentially functional genes and at least 8 pseudogenes. The IFNB (n = 6), represented in human and mouse by one copy, are also present as multiple copies in Bos taurus. The IFNT, which encode a non-virally inducible, ruminant-specific IFN secreted by the pre-implantation conceptus, are represented by three genes and two pseudogenes. The latter have sequences intermediate between IFNT and IFNW. A new Type I IFN family (IFNX) of four members, one of which is a pseudogene, appears to have diverged from the IFNA lineage at least 83 million years ago, but is absent in all other sequenced genomes with the possible exception of the horse, a non-ruminant herbivore. Conclusion: In summary, we have provided the first comprehensive annotation of the Type I IFN locus in Bos taurus, thereby providing an insight into the functional evolution of the Type I IFN in ruminants. The diversity and global spread of the ruminant species may have required an expansion of the Type I IFN locus and its constituent genes to provide broad anti-viral protection required for foraging and foregut fermentation.

关键词： Gene Conversion basic local alignment search tool Bovine Genome Ruminant Species Whole Genome Shotgun Sequence

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Hymenoptera Genome Database: new genomes and annotation datasets for improved go enrichment and orthologue analyses

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NUCLEIC ACIDS REsearch 2022年第D1期50卷 D1032-D1039页

作者： Walsh, Amy T. Triant, Deborah A. Le Tourneau, Justin J. Shamimuzzaman, Md Elsik, Christine G. Univ Missouri Div Anim Sci Columbia MO 65211 USA Univ Missouri Div Plant Sci & Technol Columbia MO 65211 USA Univ Missouri MU Inst Data Sci & Informat Columbia MO 65211 USA

We report an update of the Hymenoptera Genome Database (HGD: http://*** ), a genomic database of hymenopteran insect species. The number of species represented in HGD has nearly tripled, with fifty-eight hymenopteran species, including twenty bees, twenty-three ants, eleven wasps and four sawflies. With a reorganized website, HGD continues to provide the HymenopteraMine genomic data mining warehouse and JBrowse/ Apollo genome browsers integrated with BLAST. We have computed Gene Ontology (GO) annotations for all species, greatly enhancing the GO annotation data gathered from UniProt with more than a ten-fold increase in the number of GO-annotated genes. We have also generated orthology datasets that encompass all HGD species and provide orthologue clusters for fourteen taxonomic groups. The new GO annotation and orthology data are available for searching in HymenopteraMine, and as bulk file downloads.

关键词： ants bees genes genome hymenoptera insecta wasps data mining basic local alignment search tool datasets

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Genometrics as an essential tool for the assembly of whole genome sequences:: the example of the chromosome of Bifidobacterium longum NCC2705 -: art. no. 60

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BMC MICROBIOLOGY 2005年第1期5卷 60-60页

作者： Guy, L Karamata, D Moreillon, P Roten, CAH Univ Lausanne Fac Biol & Med Dept Microbiol Fondamentale CH-1015 Lausanne Switzerland

Background: Analysis of the first reported complete genome sequence of Bifidobacterium longum NCC2705, an actinobacterium colonizing the gastrointestinal tract, uncovered its proteomic relatedness to Streptomyces coelicolor and Mycobacterium tuberculosis. However, a rapid scrutiny by genometric methods revealed a genome organization totally different from all so far sequenced high-GC Gram-positive chromosomes. Results: Generally, the cumulative GC- and ORF orientation skew curves of prokaryotic genomes consist of two linear segments of opposite slope: the minimum and the maximum of the curves correspond to the origin and the terminus of chromosome replication, respectively. However, analyses of the B. longum NCC2705 chromosome yielded six, instead of two, linear segments, while its dnaA locus, usually associated with the origin of replication, was not located at the minimum of the curves. Furthermore, the coorientation of gene transcription with replication was very low. Comparison with closely related actinobacteria strongly suggested that the chromosome of B. longum was misassembled, and the identification of two pairs of relatively long homologous DNA sequences offers the possibility for an alternative genome assembly proposed here below. By genometric criteria, this configuration displays all of the characters common to bacteria, in particular to related high-GC Gram-positives. In addition, it is compatible with the partially sequenced genome of DJO10A B. longum strain. Recently, a corrected sequence of B. longum NCC2705, with a configuration similar to the one proposed here below, has been deposited in GenBank, confirming our predictions. Conclusion: Genometric analyses, in conjunction with standard bioinformatic tools and knowledge of bacterial chromosome architecture, represent fast and straightforward methods for the evaluation of chromosome assembly.

关键词： basic local alignment search tool Insertion Sequence Yersinia Pestis rRNA Operon Chromosome Replication

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Dramatic down-regulation of oxidoreductases in human hepatocellular carcinoma hepG2 cells: proteomics and gene ontology unveiling new frontiers in cancer enzymology

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PROTEOME SCIENCE 2008年第1期6卷 29-29页

作者： Ngoka, Lambert C. M. Virginia Commonwealth Univ Dept Chem Richmond VA 23284 USA Texas Tech Univ Hlth Sci Ctr Paul L Foster Sch Med Dept Biomed Sci Lubbock TX 79409 USA

Background: Oxidoreductases are enzymes that catalyze many redox reactions in normal and neoplastic cells. Their actions include catalysis of the transformation of free, neutral oxygen gas into oxygen free radicals, superoxide, hydroperoxide, singlet oxygen and hydrogen peroxide. These activated forms of oxygen contribute to oxidative stress that modifies lipids, proteins, DNA and carbohydrates. On the other hand, oxidoreductases constitute one of the most important free radical scavenger systems typified by catalase, superoxide dismutase and glutathione peroxidase. In this work, proteomics, Gene Ontology mapping and Directed Acyclic Graphs (DAG) are employed to detect and quantify differential oxidoreductase enzyme expressions between HepG2 cells and normal human liver tissues. Results: For the set of bioinformatics calculations whose BLAST searches are performed using the BLAST program BLASTP 2.2.13 [Nov-27-2005], DAG of the Gene Ontology's Molecular Function annotations show that oxidoreductase activity parent node of the liver proteome contains 331 annotated protein sequences, 7 child nodes and an annotation score of 188.9, whereas that of HepG2 cells has 188 annotated protein sequences, 3 child nodes and an annotation score of only 91.9. Overwhelming preponderance of oxidoreductases in the liver is additionally supported by the isomerase DAGs: nearly all the reactions described in the normal liver isomerase DAG are oxidoreductase isomerization reactions, whereas only one of the three child nodes in the HepG2 isomerase DAG is oxidoreductase. Upon normalization of the annotation scores to the parent Molecular Function nodes, oxidoreductases are down-regulated in HepG2 cells by 58%. Similarly, for the set of bioinformatics calculations whose BLAST searches are carried out using BLASTP 2.2.15 [Oct-15-2006], oxidoreductases are down-regulated in HepG2 cells by 56%. Conclusion: Proteomics and Gene Ontology reveal, for the first time, differential enzyme activities be

关键词： Gene Ontology HepG2 Cell Child Node basic local alignment search tool Oxidoreductase Activity

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Complete genome of Staphylococcus aureus Tager 104 provides evidence of its relation to modern systemic hospital-acquired strains

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BMC GENOMICS 2016年第1期17卷 179-179页

作者： Davis, Richard W. Brannen, Andrew D. Hossain, Mohammad J. Monsma, Scott Bock, Paul E. Nahrendorf, Matthias Mead, David Lodes, Michael Liles, Mark R. Panizzi, Peter Auburn Univ Harrison Sch Pharm Dept Drug Discovery & Dev 4306 Walker Bldg Auburn AL 36849 USA Auburn Univ Dept Biol Sci 101 Rouse Life Sci Bldg Auburn AL 36849 USA Lucigen Corp 2905 Parmenter St Middleton WI 53562 USA Vanderbilt Univ Med Ctr Dept Pathol Microbiol & Immunol Nashville TN 37232 USA Massachusetts Gen Hosp Ctr Syst Biol Simches Res Bldg185 Cambridge St Boston MA 02114 USA Harvard Univ Sch Med Simches Res Bldg185 Cambridge St Boston MA 02114 USA

Background: Staphylococcus aureus (S. aureus) infections range in severity due to expression of certain virulence factors encoded on mobile genetic elements (MGE). As such, characterization of these MGE, as well as single nucleotide polymorphisms, is of high clinical and microbiological importance. To understand the evolution of these dangerous pathogens, it is paramount to define reference strains that may predate MGE acquisition. One such candidate is S. aureus Tager 104, a previously uncharacterized strain isolated from a patient with impetigo in 1947. Results: We show here that S. aureus Tager 104 can survive in the bloodstream and infect naive organs. We also demonstrate a procedure to construct and validate the assembly of S. aureus genomes, using Tager 104 as a proof-of-concept. In so doing, we bridged confounding gap regions that limited our initial attempts to close this 2.82 Mb genome, through integration of data from Illumina Nextera paired-end, PacBio RS, and Lucigen NxSeq mate-pair libraries. Furthermore, we provide independent confirmation of our segmental arrangement of the Tager 104 genome by the sole use of Lucigen NxSeq libraries filled by paired-end MiSeq reads and alignment with SPAdes software. Genomic analysis of Tager 104 revealed limited MGE, and vSa beta island configuration that is reminiscent of other hospital acquired S. aureus genomes. Conclusions: Tager 104 represents an early-branching ancestor of certain hospital-acquired strains. Combined with its earlier isolation date and limited content of MGE, Tager 104 can serve as a viable reference for future comparative genome studies.

关键词： basic local alignment search tool Minimum Inhibitory Concentration Mobile Genetic Element Genomic Island Illumina MiSeq

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Genetic diversity and C2-like subgenogroup strains of enterovirus 71, Taiwan, 2008

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VIROLOGY JOURNAL 2010年第1期7卷 277-277页

作者： Huang, Yuan-Pin Lin, Tsuey-Li Hsu, Li-Ching Chen, Yu-Ju Tseng, Yin-Hsin Hsu, Chiu-Chu Fan, Wen-Bin Yang, Jyh-Yuan Chang, Feng-Yee Wu, Sheng Ctr Dis Control Res & Diagnost Ctr Dept Hlth Taipei Taiwan Taipei Med Univ Sch Med Lab Sci & Biotechnol Taipei Taiwan

Background: Human enterovirus 71 (EV-71) is known of having caused numerous outbreaks of hand-foot-mouth disease, and other clinical manifestations globally. In 2008, 989 EV-71 strains were isolated in Taiwan. Results: In this study, the genetic and antigenic properties of these strains were analyzed and the genetic diversity of EV-71 subgenogroups surfacing in Taiwan was depicted, which includes 3 previously reported subgenogroups of C5, B5, and C4, and one C2-like subgenogroup. Based on the phylogenetic analyses using their complete genome nucleotide sequences and neutralization tests, the C2-like subgenogroup forms a genetically distinct cluster from other subgenogroups, and the antisera show a maximum of 128-fold decrease of neutralization titer against this subgenogroup. In addition, the subgenogroup C4 isolates of 2008 were found quite similar genetically to the Chinese strains that caused outbreaks in recent years and thus they should be carefully watched. Conclusions: Other than to be the first report describing the existence of C2-like subgenogroup of EV-71 in Taiwan, this article also foresees a potential of subgenogroup C4 outbreaks in Taiwan in the near future.

关键词： basic local alignment search tool Neutralization Antibody Titer Human Rhinovirus Human Enterovirus Elicit Neutralize Antibody

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Analyses of murine GBP homology clusters based on in silico, in vitro and in vivo studies

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BMC GENOMICS 2008年第1期9卷 158-158页

作者： Kresse, Alexandra Konermann, Carolin Degrandi, Daniel Beuter-Gunia, Cornelia Wuerthner, Jan Pfeffer, Klaus Beer, Sandra Univ Dusseldorf Inst Med Microbiol D-40225 Dusseldorf Germany Univ Dusseldorf Hosp Hyg D-40225 Dusseldorf Germany

The interactions between pathogens and hosts lead to a massive upregulation of antimicrobial host effector molecules. Among these, the 65 kDa guanylate binding proteins (GBPs) are interesting candidates as intricate components of the host effector molecule repertoire. Members of the GBP family are highly conserved in vertebrates. Previous reports indicate an antiviral activity of human GBP1 (hGBP1) and murine GBP2 (mGBP2). We recently demonstrated that distinct murine GBP (mGBP) family members are highly upregulated upon Toxoplasma gondii infection and localize around the intracellular protozoa T. gondii. Moreover, we characterised five new mGBP family members within the murine 65 kDa GBP family. Here, we identified a new mGBP locus named mGbp11. Based on bacterial artificial chromosome (BAC), expressed sequence tag (EST), and RTPCR analyses this study provides a detailed insight into the genomic localization and organization of the mGBPs. These analyses revealed a 166-kb spanning region on chromosome 3 harboring five transcribed mGBPs (mGbp1, mGbp2, mGbp3, mGbp5, and mGbp7) and one pseudogene (pseudomGbp1), as well as a 332-kb spanning region on chromosome 5 consisting of six transcribed mGBPs (mGbp4, mGbp6, mGbp8, mGbp9, mGbp10, and mGbp11), and one pseudogene (pseudomgbp2). Besides the strikingly high homology of 65% to 98% within the coding sequences, the mGBPs on chromosome 5 cluster also exhibit a highly homologous exon-intron structure whereas the mGBP on chromosome 3 reveals a more divergent exon-intron structure. This study details the comprehensive genomic organization of mGBPs and suggests that a continuously changing microbial environment has exerted evolutionary pressure on this gene family leading to multiple gene amplifications. A list of links for this article can be found in the Availability and requirements section.

关键词： Bacterial Artificial Chromosome basic local alignment search tool Bacterial Artificial Chromosome Sequence Guanylate Binding Protein CaaX Motif

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