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Gene Family (gene + family)
Kinds of Gene Family Selected AbstractsmRNA Encoding a Putative RNA Helicase of the DEAD-Box Gene Family is Up-Regulated in Trypomastigotes of Trypanosoma cruziTHE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 6 2000ALBERTO M. DÍAZ AÑEL ABSTRACT. Differential display of mRNAs from Trypanosoma cruzi epimastigote and metacyclic trypomastigote stages showed several mRNA species differing in their expression level. The cDNA corresponding to one of these mRNAs was used as a probe in Northern blots and identified a RNA product of 2.6 kb with an expression level eight or more times higher in trypomastigotes than in epimastigotes. This probe was also used to screen a genomic library of T. cruzi CL Brener clone prepared in lambda FIX. A clone of about 15 kb was selected that, after partial sequencing, revealed an open reading frame of 688 amino acids encoding a deduced protein with similarity to RNA helicases of the DEAD-box gene family. The presence of the eight conserved motifs characteristic of the DEAD protein family was observed in the T. cruzi sequence, indicating that it corresponds to a putative RNA helicase gene, which we named HelTc. Southern blot analysis indicated that HelTc is a single-copy gene. Pulsed-field gel electrophoresis separation of chromosomes of several isolates of T. cruzi showed that this gene was localized in one or two chromosomal bands. [source] The archaeal flagellum: a different kind of prokaryotic motility structureFEMS MICROBIOLOGY REVIEWS, Issue 2 2001Nikhil A Thomas Abstract The archaeal flagellum is a unique motility apparatus distinct in composition and likely in assembly from the bacterial flagellum. Gene families comprised of multiple flagellin genes co-transcribed with a number of conserved, archaeal-specific accessory genes have been identified in several archaea. However, no homologues of any bacterial genes involved in flagella structure have yet been identified in any archaeon, including those archaea in which the complete genome sequence has been published. Archaeal flagellins possess a highly conserved hydrophobic N-terminal sequence that is similar to that of type IV pilins and clearly unlike that of bacterial flagellins. Also unlike bacterial flagellins but similar to type IV pilins, archaeal flagellins are initially synthesized with a short leader peptide that is cleaved by a membrane-located peptidase. With recent advances in genetic transfer systems in archaea, knockouts have been reported in several genes involved in flagellation in different archaea. In addition, techniques to isolate flagella with attached hook and anchoring structures have been developed. Analysis of these preparations is under way to identify minor structural components of archaeal flagella. This and the continued isolation and characterization of flagella mutants should lead to significant advances in our knowledge of the composition and assembly of archaeal flagella. [source] Comparative genomics of the Mill family: a rapidly evolving MHC class,I gene familyEUROPEAN JOURNAL OF IMMUNOLOGY, Issue 6 2004Yutaka Watanabe Abstract Mill (MHC class,I-like located near the leukocyte receptor complex) is a novel family of class,I genes identified in mice that is most closely related to the human MICA/B family. In the present study, we isolated Mill cDNA from rats and carried out a comparative genomic analysis. Rats have two Mill genes orthologous to mouse Mill1 and Mill2 near the leukocyte receptor complex, with expression patterns similar to those of their mouse counterparts. Interspecies sequence comparison indicates that Mill is one of the most rapidly evolving class,I gene families and that non-synonymous substitutions occur more frequently than synonymous substitutions in its ,,1 domain, implicating the involvement of Mill in immune defenses. Interestingly, the ,,2 domain of rat Mill2 contains a premature stop codon in many inbred strains, indicating that Mill2 is not essential for survival. A computer search of the database identified a horse Mill -like expressed sequence tag, indicating that Mill emerged before the radiation of mammals. Hence, the failure to find Mill in human indicates strongly that it was lost from the human lineage. Our present work provides convincing evidence that Mill is akin to the MICA/B family, yet constitutes a distinctgene family. [source] ALLELIC DIVERGENCE PRECEDES AND PROMOTES GENE DUPLICATIONEVOLUTION, Issue 5 2006Stephen R. Proulx Abstract One of the striking observations from recent whole-genome comparisons is that changes in the number of specialized genes in existing gene families, as opposed to novel taxon-specific gene families, are responsible for the majority of the difference in genome composition between major taxa. Previous models of duplicate gene evolution focused primarily on the role that neutral processes can play in evolutionary divergence after the duplicates are already fixed in the population. By instead including the entire cycle of duplication and divergence, we show that specialized functions are most likely to evolve through strong selection acting on segregating alleles at a single locus, even before the duplicate arises. We show that the fitness relationships that allow divergent alleles to evolve at a single locus largely overlap with the conditions that allow divergence of previously duplicated genes. Thus, a solution to the paradox of the origin of organismal complexity via the expansion of gene families exists in the form of the deterministic spread of novel duplicates via natural selection. [source] Otx1 gene-controlled morphogenesis of the horizontal semicircular canal and the origin of the gnathostome characteristicsEVOLUTION AND DEVELOPMENT, Issue 4 2000Sylvie Mazan SUMMARY The horizontal semicircular canal of the inner ear is a unique feature of gnathostomes and is predated by the two vertical semicircular canals, which are already present in lampreys and some fossil, armored jawless vertebrates regarded as close relatives of gnathostomes. Inactivation in mice of the orthodenticle -related gene Otx1 results in the absence of this structure. In bony fishes and tetrapods (osteichthyans), this gene belongs to a small multigene family comprising at least two orthology classes, Otx1 and Otx2. We report that, as in the mouse, xenopus and zebrafish, Otx1- and Otx2 -related genes are present in a chondrichthyan, the dogfish Scyliorhinus canicula, with an Otx1 expression domain in the otocyst very similar to those observed in osteichthyans. A strong correlation is thus observed in extant vertebrates between the distribution of the horizontal semicircular canal and the presence of an Otx1 ortholog expressed in the inner ear, which supports the hypothesis that the absence of this characteristic in Otx1 -/- mice may correspond to an atavism. The same conclusion applies to two other gnathostome-specific characteristics also deleted in Otx1 -/- mice, the utriculosaccular duct and the ciliary process. Together with functional analyses of Otx1 and Otx2 genes in mice and comparative analyses of the Otx gene families characterized in chordates, these discoveries lead to the hypothesis that some of the anatomic characteristics of gnathostomes have appeared quite suddenly and almost simultaneously in vertebrate evolution, possibly as a consequence of gene functional diversifications following duplications of an ancestral chordate gene. [source] Molecular physiology of SLC4 anion exchangersEXPERIMENTAL PHYSIOLOGY, Issue 1 2006Seth L. Alper Plasmalemmal Cl,,HCO3, exchangers regulate intracellular pH and [Cl,] and cell volume. In polarized epithelial cells, they contribute also to transepithelial secretion and reabsorption of acid,base equivalents and of Cl,. Members of both the SLC4 and SLC26 mammalian gene families encode Na+ -independent Cl,,HCO3, exchangers. Human SLC4A1/AE1 mutations cause either the erythroid disorders spherocytic haemolytic anaemia or ovalocytosis, or distal renal tubular acidosis. SLC4A2/AE2 knockout mice die at weaning. Human SLC4A3/AE3 polymorphisms have been associated with seizure disorder. Although mammalian SLC4/AE polypeptides mediate only electroneutral Cl,,anion exchange, trout erythroid AE1 also promotes osmolyte transport and increased anion conductance. Mouse AE1 is required for DIDS-sensitive erythroid Cl, conductance, but definitive evidence for mediation of Cl, conductance is lacking. However, a single missense mutation allows AE1 to mediate both electrogenic SO42,,Cl, exchange or electroneutral, H+ -independent SO42,,SO42, exchange. In the Xenopus oocyte, the AE1 C-terminal cytoplasmic tail residues reported to bind carbonic anhydrase II are dispensable for Cl,,Cl, exchange, but required for Cl,,HCO3, exchange. AE2 is acutely and independently inhibited by intracellular and extracellular H+, and this regulation requires integrity of the most highly conserved sequence of the AE2 N-terminal cytoplasmic domain. Individual missense mutations within this and adjacent regions identify additional residues which acid-shift pHo sensitivity. These regions together are modelled to form contiguous surface patches on the AE2 cytoplasmic domain. In contrast, the N-terminal variant AE2c polypeptide exhibits an alkaline-shifted pHo sensitivity, as do certain transmembrane domain His mutants. AE2-mediated anion exchange is also stimulated by ammonium and by hypertonicity by a mechanism sensitive to inhibition by chelation of intracellular Ca2+ and by calmidazolium. This growing body of structure,function data, together with increased structural information, will advance mechanistic understanding of SLC4 anion exchangers. [source] Genetic variation, nucleotide diversity, and linkage disequilibrium in seven telomere stability genes suggest that these genes may be under constraint,,HUMAN MUTATION, Issue 4 2005Sharon A. Savage Abstract To maintain chromosomal integrity and to protect the ends of chromosomes against recognition as damaged DNA, end-to-end fusion, or recombination, a coordinated set of genes is required to stabilize the telomere. We surveyed common genetic variation in seven genes that are vital to telomere stability (TERT, POT1, TNKS, TERF1, TINF2, TERF2, and TERF2IP) and validated single nucleotide polymorphisms (SNPs) in four different ethnic groups (n=118 total). Overall, our data show limited degrees of nucleotide diversity in comparison with data from other gene families. We observed that these genes are highly conserved in sequence between species, and that for nearly all of the coding SNPs the most common allele is ancestral (i.e., it is observed in primate sequences). Our findings support the hypothesis that genetic variation in a pathway that is critical for telomere stability may be under constraint. These data establish a foundation for further investigation of these genes in population-genetics, evolution, and disease-association studies. Hum Mutat 26(4), 343,350, 2005. Published 2005, Wiley-Liss, Inc. [source] The genomic context of natural killer receptor extended gene familiesIMMUNOLOGICAL REVIEWS, Issue 1 2001John Trowsdale Summary: The two sets of inhibitory and activating natural killer (NK) receptor genes belong either to the Ig or to the C-type lectin superfamilies. Both are extensive and diverse, comprising genes of varying degrees of relatedness, indicative of a process of iterative duplication. We have constructed gene maps to help understand how and when NK receptor genes developed and the nature of their polymorphism. A cluster of over 15 C-type lectin genes, the natural killer complex is located on human chromosome 12p13.1, syntenic with a region in mouse that borders multiple Ly49 loci. The equivalent locus in man is occupied by a single pseudogene, LY49L. The immunoglobulin superfamily of loci, the leukocyte receptor complex (LRC), on chromosome 19q13.4, contains many polymorphic killer cell immunoglobulin-like receptor (KIR) genes as well as multiple related sequences. These include immunoglobulin-like transcript (ILT) (or leukocyte immunoglobulin-like receptor genes), leukocyte-associated inhibitory receptor genes (LAIR), NKp46, Fc,R and the platelet glycoprotein receptor VI locus, which encodes a collagen-binding molecule. KIRs are expressed mostly on NK cells and some T cells. The other LRC loci are more widely expressed. Further centromeric of the LRC are sets of additional loci with weak sequence similarity to the KIRs, including the extensive CD66(CEA) and Siglec families. The LRC-syntenic region in mice contains no orthologues of KIRs. Some of the KIR genes are highly polymorphic in terms of sequence as well as for presence/absence of genes on different haplotypes. Some anchor loci, such as KIR2DL4, are present on most haplotypes. A few ILT loci, such as ILT5 and ILT8, are polymorphic, but only ILT6 exhibits presence/absence variation. This knowledge of the genomic organisation of the extensive NK superfamilies underpins efforts to understand the functions of the encoded NK receptor molecules. It leads to the conclusion that the functional homology of human KIR and mouse Ly49 genes arose by convergent evolution. NK receptor immunogenetics has interesting parallels with the major histocompatibility complex (MHC) in which some of the polymorphic genes are ligands for NK molecules. There are hints of an ancient genetic relationship between NK receptor genes and MHC-paralogous regions on chromosomes 1, 9 and 19. The picture that emerges from both complexes is of eternal evolutionary restlessness, presumably in response to resistance to disease. This work was funded by the Wellcome Trust and the MRC [source] Cloning and characterization of an immunoglobulin A Fc receptor from cattleIMMUNOLOGY, Issue 2 2004H. Craig Morton Summary Here, we describe the cloning, sequencing and characterization of an immunoglobulin A (IgA) Fc receptor from cattle (bFc,R). By screening a translated EST database with the protein sequence of the human IgA Fc receptor (CD89) we identified a putative bovine homologue. Subsequent polymerase chain reaction (PCR) amplification confirmed that the identified full-length cDNA was expressed in bovine cells. COS-1 cells transfected with a plasmid containing the cloned cDNA bound to beads coated with either bovine or human IgA, but not to beads coated with bovine IgG2 or human IgG. The bFc,R cDNA is 873 nucleotides long and is predicted to encode a 269 amino-acid transmembrane glycoprotein composed of two immunoglobulin-like extracellular domains, a transmembrane region and a short cytoplasmic tail devoid of known signalling motifs. Genetically, bFc,R is more closely related to CD89, bFc,2R, NKp46, and the KIR and LILR gene families than to other FcRs. Moreover, the bFc,R gene maps to the bovine leucocyte receptor complex on chromosome 18. Identification of the bFc,R will aid in the understanding of IgA,Fc,R interactions, and may facilitate the isolation of Fc,R from other species. [source] Phage display of human antibodies from a patient suffering from coeliac disease and selection of isotype-specific scFv against gliadinIMMUNOLOGY, Issue 2 2003Claudio Rhyner Summary Coeliac disease (CD), a gastrointestinal illness characterized by intestinal malabsorption, results from gluten intolerance accompanied with immunological responses towards gliadin, an ethanol-soluble protein fraction of wheat and other cereals. The role of gliadin in eliciting immune responses in CD is still partly unclear; however, the occurrence of anti-gliadin in the sera of patients suffering from CD correlates well with clinical symptoms. In this work we report the construction of isotype-specific, phage-displayed scFv libraries from peripheral blood lymphocytes of a patient with CD and from a healthy control individual. VH and VL chains were amplified by reverse transcription,polymerase chain reaction (RT,PCR) using a set of oligonucleotides recognizing all human variable gene families. The three scFv libraries (IgA, IgG and IgM) were selectively enriched for gliadin-binding phage. After four rounds of affinity selection, polyclonal enrichment of gliadin-binding phage was observed in all libraries from the CD patient but in none from the healthy donor. Phagemid particles generated from single clones were demonstrated to be gliadin-specific, as shown by strongly positive enzyme-linked immunosorbent assay (ELISA) and BiaCore signals. The VH and VL chains from samples of these monoclonal isotype-specific phage were sequenced to identify the most common variable regions used by the immune system to elicit antibody responses against gliadin. [source] Molecular phylogenetic evidence for an extracellular Cu Zn superoxide dismutase gene in insectsINSECT MOLECULAR BIOLOGY, Issue 6 2004J. D. Parker Abstract Representatives of three ancient gene families of the antioxidant enzyme superoxide dismutase (SOD) can be found in most metazoans. In mammals and Caenorhabditis elegans, there is at least one gene each of the cytoplasmic, mitochondrial and extracellular lineages of SOD genes. The cytoplasmic SOD was one of the first enzymes to be implicated in ageing due to its protection against damaging oxygen free radicals. In contrast to other metazoans, insects were thought to lack a gene for the extracellular SOD. We have cloned and sequenced an SOD mRNA in the ant Lasius niger that appears to belong to this extracellular family. Subsequent searches and analyses of SOD gene sequences in insect databases revealed that insects do indeed express all three SOD genes including the extracellular form. We conclude that insects as well as other metazoans appear to have the full repertoire of the three families of SOD. [source] Interactions between FGF and Wnt signals and Tbx3 gene expression in mammary gland initiation in mouse embryosJOURNAL OF ANATOMY, Issue 1 2004Maxwell C. Eblaghie Abstract Interactions between Wnts, Fgfs and Tbx genes are involved in limb initiation and the same gene families have been implicated in mammary gland development. Here we explore how these genes act together in mammary gland initiation. We compared expression of Tbx3, the gene associated with the human condition ulnar,mammary syndrome, expression of the gene encoding the dual-specificity MAPK phosphatase Pyst1/MKP3, which is an early response to FGFR1 signalling (as judged by sensitivity to the SU5402 inhibitor), and expression of Lef1, encoding a transcription factor mediating Wnt signalling and the earliest gene so far known to be expressed in mammary gland development. We found that Tbx3 is expressed earlier than Lef1 and that Pyst1 is also expressed early but only transiently. Patterns of expression of Tbx3, Pyst1 and Lef1 in different glands suggest that the order of mammary gland initiation is 3, 4, 1, 2 and 5. Consistent with expression of Pyst1 in the mammary gland, we detected expression of Fgfr1b, Fgf8 and Fgf9 in both surface ectoderm and mammary bud epithelium, and Fgf4 and Fgf17 in mammary bud epithelium. Beads soaked in FGF-8 applied to the flank of mouse embryos, at a stage just prior to mammary bud initiation, induce expression of Pyst1 and Lef1 and maintain Tbx3 expression in flank tissue surrounding the bead. Grafting beads soaked in the FGFR1 inhibitor, SU5402, abolishes Tbx3, Pyst1 and Lef1 expression, supporting the idea that FGFR1 signalling is required for early mammary gland initiation. We also showed that blocking Wnt signalling abolishes Tbx3 expression but not Pyst1 expression. These data, taken together with previous findings, suggest a model in which Tbx3 expression is induced and maintained in early gland initiation by both Wnt and Fgf signalling through FGFR1. [source] P1 Regionalisation of the brain as an evolutionarily conserved developmental mechanism.JOURNAL OF ANATOMY, Issue 1-2 2001E. GALE Comparative studies of chordate neural connectivity and gene families have provided evidence for evolutionary conservation of the patterning mechanisms in brain development (review Holland & Holland, Curr. Opin. Neurobiol.9, 1999). Based on expression patterns of ascidian and amphioxus homologues of the Otx gene and the Hox1 gene and of the ascidian Pax-2/5/8, the chordate brain has been suggested to have tripartite development (Wada et al., Development125, 1998; Kozmik et al., Development126, 1999). Primitively, the chordates have regions homologous to the vertebrate forebrain, anterior midbrain and posterior hindbrain while the posterior midbrain/anterior hindbrain region seems to be a vertebrate innovation. The extent of the homologies within each of these regions between the vertebrates and their ancestors is not fully determined but the similarity of Hox gene expression patterns suggests organisational constants over evolutionary time within the posterior hindbrain region. Identification of the posterior hindbrain region as a developmental unit in vertebrates is demonstrated in the retinoid-deficient quail. Embryos laid by quails fed a retinoid-deficient diet have no posterior hindbrain while the anterior hindbrain is specified normally. Through DiI cell lineage tracing and a temporal analysis of gene expression characteristic of this region (Krox-20, Hoxb-1, mafB, and fgf3), we have followed the development of this region of cells. From the initial formation of the neural plate phenotype in the retinoid-deficient quail, there is no evidence of a posterior hindbrain. This region is never specified and all the cells of the hindbrain participate in an anterior hindbrain fate. A single retinoid injection in ovo during early development completely rescues the posterior hindbrain ensuring that the phenotype was the result of a single stimulus. Therefore cells from the posterior hindbrain respond in a coordinated regional manner to the presence or absence of a single gene inducer, retinoic acid. We present evidence of regionalisation of the vertebrate head that is up stream of segment specification. In combination with data from amphioxus and ascidians, this may represent a common mechanism for head development throughout chordate evolution. Interestingly, regional deletion with enlargement of the adjacent region is very reminiscent of the gap gene phenotype in Drosophila. It would be disregarding millions of years of divergent evolution to suggest that vitamin A is identical to a Drosophila gap gene inducer; nevertheless this data supports the hypothesis of common underlying regulation of axial regionalisation and gene hierarchies. [source] Pim-1 kinase phosphorylates and stabilizes RUNX3 and alters its subcellular localizationJOURNAL OF CELLULAR BIOCHEMISTRY, Issue 4 2008Hye-Ryun Kim Abstract The loci of the Pim and Runx gene families have been identified as targets for viral insertions in CD2-myc mice. Synergistic cooperation between Pim and RUNX was also found in the CD2-Runx2 transgenic mouse lymphoma model. RUNX genes have come to prominence recently because of their roles as essential regulators of cell fate in development. Paradoxically, they appear to function either as tumor-suppressor genes or dominant oncogenes according to the cellular context. However, the molecular mechanism of the ambiguous roles played by this family of transcription factors in cancer has remained largely uninvestigated. Here we demonstrate that Pim-1 phosphorylates four Ser/Thr residues within the Runt domain and stabilizes RUNX3 protein. In addition, Pim-1 markedly altered the cellular localization of RUNX3 from the nucleus to the cytoplasm. Our results demonstrate that the subcellular localization of RUNX3 is altered by phosphorylation. We propose that RUNX family members may behave as oncogenes if mislocalized to a cellular micro-compartment. J. Cell. Biochem. 105: 1048,1058, 2008. © 2008 Wiley-Liss, Inc. [source] Object-oriented approach to drug design enabled by NMR SOLVE: First real-time structural tool for characterizing protein,ligand interactionsJOURNAL OF CELLULAR BIOCHEMISTRY, Issue S37 2001Daniel S. Sem Abstract As a result of genomics efforts, the number of protein drug targets is expected to increase by an order of magnitude. Functional genomics efforts are identifying these targets, while structural genomics efforts are determining structures for many of them. However, there is a significant gap in going from structural information for a protein target to a high affinity (Kd,<,100 nM) inhibitor, and the problem is multiplied by the sheer number of new targets now available. nature frequently designs proteins in classes that are related by the reuse, through gene duplication events, of cofactor binding domains. This reuse of functional domains is an efficient way to build related proteins in that it is object-oriented. There is a growing realization that the most efficient drug design strategies for attacking the mass of targets coming from genomics efforts will be systems-based approaches that attack groups of related proteins in parallel. We propose that the most effective drug design strategy will be one that parallels the object-oriented manner by which nature designed the gene families themselves. IOPE (Integrated Object-Oriented PharmacoEngineering) is such an approach. It is a three-step technology to build focused combinatorial libraries of potential inhibitors for major families and sub-families of enzymes, using cogent NMR data derived from representatives of these protein families. The NMR SOLVE (Structurally Oriented Library Valency Engineering) data used to design these libraries are gathered in days, and data can be obtained for large proteins (>,170 kDa). Furthermore, the process is fully object-oriented in that once a given bi-ligand is identified for a target, potency is retained if different cofactor mimics are swapped. This gives the drug design process maximum flexibility, allowing for the more facile transition from in vitro potency to in vivo efficacy. J. Cell. Biochem. Suppl. 37: 99,105, 2001. © 2002 Wiley-Liss, Inc. [source] Sigma factor selectivity in Borrelia burgdorferi: RpoS recognition of the ospE/ospF/elp promoters is dependent on the sequence of the ,10 regionMOLECULAR MICROBIOLOGY, Issue 6 2006Christian H. Eggers Summary Members of the ospE/ospF/elp lipoprotein gene families of Borrelia burgdorferi, the Lyme disease agent, are transcriptionally upregulated in response to the influx of blood into the midgut of an infected tick. We recently have demonstrated that despite the high degree of similarity between the promoters of the ospF (PospF) and ospE (PospE) genes of B. burgdorferi strain 297, the differential expression of ospF is RpoS-dependent, while ospE is controlled by ,70. Herein we used wild-type and RpoS-deficient strains of B. burgdorferi and Escherichia coli to analyse transcriptional reporters consisting of a green fluorescent protein (gfp) gene fused to PospF, PospE, or two hybrid promoters in which the ,10 regions of PospF and PospE were switched [PospF (E , 10) and PospE,(F , 10) respectively]. We found that the PospF,10 region is both necessary and sufficient for RpoS-dependent recognition in B. burgdorferi, while ,70 specificity for PospE is dependent on elements outside of the ,10 region. In E. coli, sigma factor selectivity for these promoters was much more permissive, with expression of each being primarily due to ,70. Alignment of the sequences upstream of each of the ospE/ospF/elp genes from B. burgdorferi strains 297 and B31 revealed that two B31 ospF paralogues [erpK (BBM38) and erpL (BBO39)] have ,10 regions virtually identical to that of PospF. Correspondingly, expression of gfp reporters based on the erpK and erpL promoters was RpoS-dependent. Thus, the sequence of the PospF,10 region appears to serve as a motif for RpoS recognition, the first described for any B. burgdorferi promoter. Taken together, our data support the notion that B. burgdorferi utilizes sequence differences at the ,10 region as one mechanism for maintaining the transcriptional integrity of RpoS-dependent and -independent genes activated at the onset of tick feeding. [source] A novel mechanism for control of antigenic variation in the haemagglutinin gene family of Mycoplasma synoviaeMOLECULAR MICROBIOLOGY, Issue 4 2000A. H. Noormohammadi High-frequency phase and antigenic variation of homologous lipoprotein haemagglutinins has been seen in both the major avian mycoplasma pathogens, Mycoplasma synoviae and Mycoplasma gallisepticum. The expression and, hence, antigenic variation of the pMGA gene family (encoding these lipoproteins in M. gallisepticum) is controlled by variation in the length of a trinucleotide repeat motif 5, to the promoter of each gene. However, such a mechanism was not detected in preliminary observations on M. synoviae. Thus, the basis for control of variation in the vlhA gene family (which encodes the homologous haemagglutinin in M. synoviae) was investigated to enable comparison with its homologue in M. gallisepticum and with other lipoprotein gene families in mycoplasmas. The start point of transcription was identified 119 bp upstream of the initiation codon, but features associated with control of transcription in other mycoplasma lipoprotein genes were not seen. Comparison of three copies of vlhA revealed considerable sequence divergence at the 3, end of the gene, but conservation of the 5, end. Southern blot analysis of M. synoviae genomic DNA revealed that the promoter region and part of the conserved 5, coding sequence occurred as a single copy, whereas the remainder of the coding sequence occurred as multiple copies. A 9.7 kb fragment of the genome was found to contain eight tandemly repeated regions partially homologous to vlhA, all lacking the putative promoter region and the single-copy 5, end of vlhA, but extending over one of four distinct overlapping regions of the 3, coding sequence. Examination of sequential clones of M. synoviae established that unidirectional recombination occurs between the pseudogenes and the expressed vlhA, with duplication of pseudogene sequence and loss of the corresponding region previously seen in the expressed gene. Expression of the 5, end of two variants of the vlhA gene showed that they differed in their reaction with monoclonal antibodies specific for this region. These data suggest that the control of vlhA antigenic variation in M. synoviae is achieved by multiple gene conversion events using a repertoire of coding sequences to generate a chimeric expressed gene, with the greatest potential for variation generated in the region encoding the haemagglutinin. Thus, completely distinct mechanisms have been adopted to control antigenic variation in homologous gene families. [source] A shared promoter region suggests a common ancestor for the human VCX/Y, SPANX, and CSAG gene families and the murine CYPT familyMOLECULAR REPRODUCTION & DEVELOPMENT, Issue 2 2008Martin A. Hansen Abstract Many testis-specific genes from the sex chromosomes are subject to rapid evolution, which can make it difficult to identify murine genes in the human genome. The murine CYPT gene family includes 15 members, but orthologs were undetectable in the human genome. However, using refined homology search, sequences corresponding to the shared promoter region of the CYPT family were identified at 39 loci. Most loci were located immediately upstream of genes belonging to the VCX/Y, SPANX, or CSAG gene families. Sequence comparison of the loci revealed a conserved CYPT promoter-like (CPL) element featuring TATA and CCAAT boxes. The expression of members of the three families harboring the CPL resembled the murine expression of the CYPT family, with weak expression in late pachytene spermatocytes and predominant expression in spermatids, but some genes were also weakly expressed in somatic cells and in other germ cell types. The genomic regions harboring the gene families were rich in direct and inverted segmental duplications (SD), which may facilitate gene conversion and rapid evolution. The conserved CPL and the common expression profiles suggest that the human VCX/Y, SPANX, and CSAG2 gene families together with the murine SPANX gene and the CYPT family may share a common ancestor. Finally, we present evidence that VCX/Y and SPANX may be paralogs with a similar protein structure consisting of C terminal acidic repeats of variable lengths. Mol. Reprod. Dev. 75: 219,229, 2008. © 2007 Wiley-Liss, Inc. [source] Origin of the murine implantation serine proteinase subfamily,MOLECULAR REPRODUCTION & DEVELOPMENT, Issue 2 2004Colleen M. O'Sullivan Abstract The S1 serine protease family is one of the largest gene families known. Within this family there are several subfamilies that have been grouped together as a result of sequence comparisons and substrate identification. The grouping of related genes allows for the speculation of function for newly found members by comparison and for novel subfamilies by contrast. Analysis of the evolutionary patterns of genes indicates whether or not orthologs are likely to be identified in other species as well as potentially indicating that hypothesized orthologs are in fact not. Looking at subtle differences between subfamily members can reveal intricacies about function and expression. Previously, we have described genes encoding two novel serine proteinases, ISP1 and ISP2, which are most closely related to tryptases. The ISP1 gene encodes the embryo-derived enzyme strypsin, which is necessary for blastocyst hatching and invasion in vitro. Additionally both ISP1 and ISP2 are co-expressed in the endometrial gland during the time of hatching, suggesting that they may also both participate in zona lysis from within the uterine lumen. Here, we demonstrate that the ISPs are tandemly linked within the tryptase cluster on 17A3.3. We suggest that remarkable similarities within the 5,-untranslated and first intron regions of ISP1 and ISP2 may explain their intimate co-regulation in uterus. We also suggest that ISP genes have evolved through gene duplication and that the ISP1 gene has also begun to adopt an additional new function in the murine preimplantation embryo. Mol. Reprod. Dev. 69: 126,136, 2004. © 2004 Wiley-Liss, Inc. [source] Hydrolytic enzymes as virulence factors of Candida albicansMYCOSES, Issue 6 2005Martin Schaller Summary Candida albicans is a facultative pathogenic micro-organism that has developed several virulence traits enabling invasion of host tissues and avoidance of host defence mechanisms. Virulence factors that contribute to this process are the hydrolytic enzymes. Most of them are extracellularly secreted by the fungus. The most discussed hydrolytic enzymes produced by C. albicans are secreted aspartic proteinases (Saps). The role of these Saps for C. albicans infections was carefully evaluated in numerous studies, whereas only little is known about the physiological role of the secreted phospholipases (PL) and almost nothing about the involvement of lipases (Lip) in virulence. They may play an important role in the pathogenicity of candidosis and their hydrolytic activity probably has a number of possible functions in addition to the simple role of digesting molecules for nutrition. Saps as the best-studied member of this group of hydrolytic enzymes contribute to host tissue invasion by digesting or destroying cell membranes and by degrading host surface molecules. There is also some evidence that hydrolytic enzymes are able to attack cells and molecules of the host immune system to avoid or resist antimicrobial activity. High hydrolytic activity with broad substrate specificity has been found in several Candida species, most notably in C. albicans. This activity is attributed to multigene families with at least 10 members for Saps and Lips and several members for PL B. Distinct members of these gene families are differentially regulated in various Candida infections. In future, prevention and control of Candida infections might be achieved by pharmacological or immunological tools specifically modulated to inhibit virulence factors, e.g. the family of Saps. [source] Managing the manganese: molecular mechanisms of manganese transport and homeostasisNEW PHYTOLOGIST, Issue 3 2005Jon K. Pittman Summary Manganese (Mn) is an essential metal nutrient for plants. Recently, some of the genes responsible for transition metal transport in plants have been identified; however, only relatively recently have Mn2+ transport pathways begun to be identified at the molecular level. These include transporters responsible for Mn accumulation into the cell and release from various organelles, and for active sequestration into endomembrane compartments, particularly the vacuole and the endoplasmic reticulum. Several transporter gene families have been implicated in Mn2+ transport, including cation/H+ antiporters, natural resistance-associated macrophage protein (Nramp) transporters, zinc-regulated transporter/iron-regulated transporter (ZRT/IRT1)-related protein (ZIP) transporters, the cation diffusion facilitator (CDF) transporter family, and P-type ATPases. The identification of mutants with altered Mn phenotypes can allow the identification of novel components in Mn homeostasis. In addition, the characterization of Mn hyperaccumulator plants can increase our understanding of how plants can adapt to excess Mn, and ultimately allow the identification of genes that confer this stress tolerance. The identification of genes responsible for Mn2+ transport has substantially improved our understanding of plant Mn homeostasis. [source] Genomics of cellulose biosynthesis in poplarsNEW PHYTOLOGIST, Issue 1 2004Chandrashekhar P. Joshi Summary Genetic improvement of cellulose production in commercially important trees is one of the formidable goals of current forest biotechnology research. To achieve this goal, we must first decipher the enigmatic and complex process of cellulose biosynthesis in trees. The recent availability of rich genomic resources in poplars make Populus the first tree genus for which genetic augmentation of cellulose may soon become possible. Fortunately, because of the structural conservation of key cellulose biosynthesis genes between Arabidopsis and poplar genomes, the lessons learned from exploring the functions of Arabidopsis genes may be applied directly to poplars. However, regulation of these genes will most likely be distinct in these two-model systems because of their inherent biological differences. This research review covers the current state of knowledge about the three major cellulose biosynthesis-related gene families from poplar genomes: cellulose synthases, sucrose synthases and korrigan cellulases. Furthermore, we also suggest some future research directions that may have significant economical impacts on global forest product industries. [source] The ABC transporter BcatrB from Botrytis cinerea is a determinant of the activity of the phenylpyrrole fungicide fludioxonilPEST MANAGEMENT SCIENCE (FORMERLY: PESTICIDE SCIENCE), Issue 5 2001T Vermeulen Abstract This study demonstrates that the ATP-binding cassette (ABC) transporter BcatrB from Botrytis cinerea influences the activity of phenylpyrrole fungicides against the pathogen. This conclusion is based on toxicity assays and northern analysis experiments which show that BcatrB replacement mutants, which do not express the BcatrB gene, show an increased sensitivity to the phenylpyrrole fungicides fludioxonil and fenpiclonil. Mutants overexpressing BcatrB exhibit a decreased sensitivity to these fungicides. In addition, accumulation of fludioxonil by BcatrB replacement mutants was higher than by wild-type isolates. For mutants overexpressing BcatrB the reverse was observed. Additional ABC and major facilitator superfamily (MFS) transporter genes were identified in an expressed sequence tag (EST) database, suggesting that B cinerea has gene families of ABC and MFS transporters. Corresponding fragments of ten ABC (BcatrC,BcatrN) and three MFS transporter genes (Bcmfs1,4) were cloned and characterised. Fludioxonil affected the transcript level of some members of these gene families in germlings during a short treatment with the fungicide at sub-lethal concentrations. Hence, other ABC and MFS transporters may affect the activity of phenylpyrrole fungicides as well. Other fungicides such as the anilinopyrimidine fungicide cyprodinil, the azole fungicide tebuconazole, the dicarboximide fungicide iprodione and the strobilurin fungicide trifloxystrobin also induced transcription of some of the ABC and MFS transporter genes identified. Therefore, we propose that various ABC and MFS transporters function in protection of the fungus against fungicides and are involved in multi-drug resistance development. © 2001 Society of Chemical Industry [source] A uniquely high number of ftsZ genes in the moss Physcomitrella patensPLANT BIOLOGY, Issue 5 2009A. Martin Abstract Plant FtsZ proteins are encoded by two small nuclear gene families (FtsZ1 and FtsZ2) and are involved in chloroplast division. From the moss Physcomitrella patens, four FtsZ proteins, two in each nuclear gene family, have been characterised and described so far. In the recently sequenced P. patens genome, we have now found a fifth ftsZ gene. This novel gene has a genomic structure similar to PpftsZ1-1. According to phylogenetic analysis, the encoded protein is a member of the FtsZ1 family, while PpFtsZ1-2, together with an orthologue from Selaginella moellendorffii, forms a separate clade. Further, this new gene is expressed in different gametophytic tissues and the encoded protein forms filamentous networks in chloroplasts, is found in stromules, and acts in plastid division. Based on all these results, we have renamed the PpFtsZ proteins of family 1 and suggest the existence of a third FtsZ family. No species is known to encode more FtsZ proteins per haploid genome than P. patens. [source] The biochemistry and biology of extracellular plant lipid-transfer proteins (LTPs)PROTEIN SCIENCE, Issue 2 2008Trevor H. Yeats Abstract Plant lipid-transfer proteins (LTPs) are abundant, small, lipid binding proteins that are capable of exchanging lipids between membranes in vitro. Despite their name, a role in intracellular lipid transport is considered unlikely, based on their extracellular localization. A number of other biological roles, including antimicrobial defense, signaling, and cell wall loosening, have been proposed, but conclusive evidence is generally lacking, and these functions are not well correlated with in vitro activity or structure. A survey of sequenced plant genomes suggests that the two biochemically characterized families of LTPs are phylogenetically restricted to seed plants and are present as substantial gene families. This review aims to summarize the current understanding of LTP biochemistry, as well as the evidence supporting the proposed in vivo roles of these proteins within the emerging post-genomic framework. [source] Gene expression changes in human cells after exposure to mobile phone microwavesPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 17 2006Daniel Remondini Abstract Possible biological effects of mobile phone microwaves were investigated in,vitro. In this study, which was part of the 5FP EU project REFLEX (Risk Evaluation of Potential Environmental Hazards From Low-Energy Electromagnetic Field Exposure Using Sensitive in,vitro Methods), six human cell types, immortalized cell lines and primary cells, were exposed to 900 and 1800,MHz. RNA was isolated from exposed and sham-exposed cells and labeled for transcriptome analysis on whole-genome cDNA arrays. The results were evaluated statistically using bioinformatics techniques and examined for biological relevance with the help of different databases. NB69 neuroblastoma cells, T,lymphocytes, and CHME5 microglial cells did not show significant changes in gene expression. In EA.hy926 endothelial cells, U937,lymphoblastoma cells, and HL-60 leukemia cells we found between 12 and 34,up- or down-regulated genes. Analysis of the affected gene families does not point towards a stress response. However, following microwave exposure, some but not all human cells might react with an increase in expression of genes encoding ribosomal proteins and therefore up-regulating the cellular metabolism. [source] cpg15 and cpg15-2 constitute a family of activity-regulated ligands expressed differentially in the nervous system to promote neurite growth and neuronal survivalTHE JOURNAL OF COMPARATIVE NEUROLOGY, Issue 5 2008Tadahiro Fujino Abstract Many ligands that affect nervous system development are members of gene families that function together to coordinate the assembly of complex neural circuits. cpg15/neuritin encodes an extracellular ligand that promotes neurite growth, neuronal survival, and synaptic maturation. Here we identify cpg15-2 as the only paralogue of cpg15 in the mouse and human genome. Both genes are expressed predominantly in the nervous system, where their expression is regulated by activity. cpg15-2 expression increases by more than twofold in response to kainate-induced seizures and nearly fourfold in the visual cortex in response to 24 hours of light exposure following dark adaptation. cpg15 and cpg15-2 diverge in their spatial and temporal expression profiles. cpg15-2 mRNA is most abundant in the retina and the olfactory bulb, as opposed to the cerebral cortex and the hippocampus for cpg15. In the retina, they differ in their cell-type specificity. cpg15 is expressed in retinal ganglion cells, whereas cpg15-2 is predominantly in bipolar cells. Developmentally, onset of cpg15-2 expression is delayed compared with cpg15 expression. CPG15-2 is glycosylphosphatidylinositol (GPI) anchored to the cell membrane and, like CPG15, can be released in a soluble-secreted form, but with lower efficiency. CPG15 and CPG15-2 were found to form homodimers and heterodimers with each other. In hippocampal explants and dissociated cultures, CPG15 and CPG15-2 promote neurite growth and neuronal survival with similar efficacy. Our findings suggest that CPG15 and CPG15-2 perform similar cellular functions but may play distinct roles in vivo through their cell-type- and tissue-specific transcriptional regulation. J. Comp. Neurol. 507:1831,1845, 2008. © 2008 Wiley-Liss, Inc. [source] Cuticular defects lead to full immunity to a major plant pathogenTHE PLANT JOURNAL, Issue 6 2007Céline Chassot Summary In addition to its role as a barrier, the cuticle is also a source of signals perceived by invading fungi. Cuticular breakdown products have been shown previously to be potent inducers of cutinase or developmental processes in fungal pathogens. Here the question was addressed as to whether plants themselves can perceive modifications of the cuticle. This was studied using Arabidopsis thaliana plants with altered cuticular structure. The expression of a cell wall-targeted fungal cutinase in A. thaliana was found to provide total immunity to Botrytis cinerea. The response observed in such cutinase-expressing plants is independent of signal transduction pathways involving salicylic acid, ethylene or jasmonic acid. It is accompanied by the release of a fungitoxic activity and increased expression of members of the lipid transfer protein, peroxidase and protein inhibitor gene families that provide resistance when overexpressed in wild-type plants. The same experiments were made in the bodyguard (bdg) mutant of A. thaliana. This mutant exhibits cuticular defects and remained free of symptoms after inoculation with B. cinerea. The expression of resistance was accompanied by the release of a fungitoxic activity and increased expression of the same genes as observed in cutinase-expressing plants. Structural defects of the cuticle can thus be converted into an effective multi-factorial defence, and reveal a hitherto hidden aspect of the innate immune response of plants. [source] Silencing a prohibitin alters plant development and senescenceTHE PLANT JOURNAL, Issue 1 2005Jen-Chih Chen Summary Prohibitins, highly conserved mitochondrial proteins, have been shown to play important roles in cell cycling and senescence in animals and yeast. Sequences with high similarity to prohibitins have been identified in a number of plant species, but their function has not yet been demonstrated. The deduced amino acid sequences of PhPHB1 and PhPHB2, sequences that we identified in a petunia floral expressed sequence tag (EST) database, show high similarity to those of prohibitin-1 and prohibitin-2 proteins, respectively, reported from yeast, animals and plants. Southern analysis suggested that these genes were members of small gene families with at least two prohibitin-1 homologs and four prohibitin-2 homologs. When we downregulated expression of prohibitin-1 using a Tobacco rattle virus-based (TRV), virus-induced gene silencing system (VIGS), we observed plants with smaller and distorted leaves and flowers. Cells in silenced flowers were larger than in control flowers, indicating a substantial reduction in the number of cell divisions that took place during corolla development. The life of silenced flowers was shorter than that of controls, whether on the plant or detached. The respiration of silenced flowers was higher than that of controls, and we observed a marked increase in the abundance of transcripts of a catalase and a small heat-shock protein in the silenced flowers. Our data indicate that prohibitins play a key role in plant development and senescence. [source] Comparative genomics of the poultry major histocompatibility complexANIMAL SCIENCE JOURNAL, Issue 2 2006Takashi SHIINA ABSTRACT This review summarizes the latest findings regarding the avian major histocompatibility complex (MHC), focusing particularly on the genomics of MHC in the Japanese quail (Cotrnix japonica) and other birds, as well as haplotype, genomics, function and disease resistance in the chicken (Gallus gallus). This information provides important insight into the breeding of disease resistance in poultry, natural selection of disease resistance in wild birds, and the effects of recombination and hitchhiking on the evolution of multiple MHC gene families. [source] | ||||||||||||||||||||||||||||||||||||||||