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PubMed1992

Evidence that eukaryotes and eocyte prokaryotes are immediate relatives.

The phylogenetic origin of eukaryotes has been unclear because eukaryotic nuclear genes have diverged substantially from prokaryotic ones. The genes coding for elongation factor EF-1 alpha were compared among various organisms. The EF-1 alpha sequences of eukaryotes contained an 11-amino acid segment that was also found in eocytes (extremely thermophilic, sulfur-metabolizing bacteria) but that was absent in all other bacteria. The related (paralogous) genes encoding elongation factor EF-2 and initiation factor IF-2 also lacked the 11-amino acid insert. These data imply that the eocytes are the closest surviving relatives (sister taxon) of the eukaryotes.

Amino Acid Sequence↗

PubMed2001

Homeobox gene clusters and the human paralogy map.

Homeobox genes encode important developmental control proteins. In vertebrates, those encoding the proteins of the HOX class and their most closely related families, including paraHOX and metaHOX classes, are clustered in paralogous regions (or paralogons). We show that the majority of the other homeobox genes (we called contraHOX) can also be clustered and belong to paralogons in humans. This suggests that they duplicated during vertebrate evolution along the same processes as the HOX genes. We tentatively assembled several paralogons in superparalogons. One of the superparalogons contains the contraHOX genes. These observations were extended to hundreds of genes, and allowed to describe a primary human genome paralogy map.

Chromosome Mapping↗

PubMedDate not supplied

The bdr gene families of the Lyme disease and relapsing fever spirochetes: potential influence on biology, pathogenesis, and evolution.

Species of the genus Borrelia cause human and animal infections, including Lyme disease, relapsing fever, and epizootic bovine abortion. The borrelial genome is unique among bacterial genomes in that it is composed of a linear chromosome and a series of linear and circular plasmids. The plasmids exhibit significant genetic redundancy and carry 175 paralogous gene families, most of unknown function. Homologous alleles on different plasmids could influence the organization and evolution of the Borrelia genome by serving as foci for interplasmid homologous recombination. The plasmid-carried Borrelia direct repeat (bdr) gene family encodes polymorphic, acidic proteins with putative phosphorylation sites and transmembrane domains. These proteins may play regulatory roles in Borrelia. We describe recent progress in the characterization of the Borrelia bdr genes and discuss the possible influence of this gene family on the biology, pathogenesis, and evolution of the Borrelia genome.

Abortion, Veterinary↗

PubMedDate not supplied

The polycystic ovary syndrome: what does insulin resistance have to do with it?

About half of infertility cases are attributable to female factors, of which anovulation is the leading cause. Most cases of anovulation are due to the polycystic ovarian syndrome (PCOS). Clinically PCOS, present in 5% of all women, consists of anovulation, acne, hirsutism, reversed LH-to-FSH ratio and often resistance to insulin. In some cases PCOS appears in familial clusters but its genetic cause is unknown. Several genes were suggested as possible culprits for PCOS but their involvement has not been proven. The central paradox regarding the role of insulin in PCOS is the high responsiveness to insulin by the ovary, as opposed to the resistance of the whole body. On the backdrop of knowledge of several paralogous genes for each of the participating proteins in the insulin signal transduction pathways, it is possible that different paralogues propagate the intracellular signal in the ovary as opposed to peripheral tissues. Studies by microarray techniques of the different gene expression profiles in the two ovarian cells and peripheral cells such as adipocytes could clarify whether the ovarian defect in PCOS is identical to the peripheral defect in insulin signal transduction, or whether serum insulin concentrations simply serve to reveal the ovarian defect.

Female↗

PubMed1994

The thyroid transcription factor-1 gene is a candidate target for regulation by Hox proteins.

Vertebrate Hox homeobox genes are transcription factors which regulate antero-posterior axial identity in embryogenesis, presumably through activation and/or repression of downstream target genes. Some of these targets were reported to code for molecules involved in cell-cell interactions, whereas no relationship has yet been demonstrated between Hox genes and other transcription factors involved in determining and/or maintaining tissue specificity. The thyroid transcription factor-1 (TTF-1) is a homeodomain-containing protein required for expression of thyroid-specific genes. A 862 bp 5' genomic fragment of the rat TTF-1 gene, conferring thyroid-specific expression to a reporter gene, was sufficient to mediate transactivation by the human HOXB3 gene in co-transfection assay in both NIH3T3 or HeLa cells. HOXB3 is expressed in early mammalian embryogenesis in the anterior neuroectoderm, branchial arches and their derivatives, including the area of the thyroid primordia and thyroid gland. Transcription of the TTF-1 promoter is induced only by HOXB3, while its paralogous gene HOXD3 or other Hox genes expressed more posteriorly (HOXA4, HOXD4, HOXC5, HOXC6, HOXC8 and Hoxd-8) have no effect. Transactivation by HOXB3 is mediated by two binding sites containing an ATTA core located at -100 and +30 from the transcription start site. DNase I footprinting experiments show that the two sites bind HOXB3 protein synthesized in both Escherichia coli and eukaryotic cells, as well as nuclear factor(s) present in protein extracts obtained from mouse embryonic tissues which express group 3 Hox genes and TTF-1. Some of the DNA-protein complexes formed by the embryonic extracts are indistinguishable from those generated by HOXB3.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

PubMed2002

ESTs as a source for sequence polymorphism discovery in sugarcane: example of the Adh genes.

Expressed sequence tags (ESTs) have proven to be a valuable tool to discover single nucleotide polymorphism (SNP) in human genes but their use for this purpose is still limited in higher plants. Using a database of approximately 250,000 sugarcane ESTs we have recovered 219 sequences encoding alcohol dehydrogenases ( Adh), which tagged 178 distinct cDNAs from 27 libraries, constructed from at least four different cultivars. The partitioning of these ESTs into paralogous genes revealed three Adh genes expressed in sugarcane, one Adh2 and two Adh1. The soundness of the partition was carefully checked by comparison to external data, especially from the closely related sorghum. Analysis of polymorphism in the alignments of EST sequences revealed a total of 37 highly reliable SNPs in the coding and untranslated regions of the three Adh genes. In the coding regions, the mean occurrence of SNPs was one for every 122 base pair. A total of eight insertion-deletions was observed, their occurrence being limited to untranslated regions. These results show that EST data constitute an invaluable source of sequence polymorphism for sugarcane that is worth carefully collecting for the future development of new marker tools.

Alcohol Dehydrogenase↗

PubMed2002

The evolution of DNA regulatory regions for proteo-gamma bacteria by interspecies comparisons.

The comparison of homologous noncoding DNA for organisms a suitable evolutionary distance apart is a powerful tool for the identification of cis regulatory elements for transcription and translation and for the study of how they assemble into functional modules. We have fit the three parameters of an affine global probabilistic alignment algorithm to establish the background mutation rate of noncoding sequence between E. coli and a series of gamma proteobacteria ranging from Salmonella to Vibrio. The lower bound we find to the neutral mutation rate is sufficiently high, even for Salmonella, that most of the conservation of noncoding sequence is indicative of selective pressures rather than of insufficient time to evolve. We then use a local version of the alignment algorithm combined with our inferred background mutation rate to assign a significance to the degree of local sequence conservation between orthologous genes, and thereby deduce a probability profile for the upstream regulatory region of all E. coli protein-coding genes. We recover 75%-85% (depending on significance level) of all regulatory sites from a standard compilation for E. coli, and 66%-85% of sigma sites. We also trace the evolution of known regulatory sites and the groups associated with a given transcription factor. Furthermore, we find that approximately one-third of paralogous gene pairs in E. coli have a significant degree of correlation in their regulatory sequence. Finally, we demonstrate an inverse correlation between the rate of evolution of transcription factors and the number of genes they regulate. Our predictions are available at http://www.physics.rockefeller.edu/([tilde-see text])siggia.

Algorithms↗

PubMed1998

Comparative analysis of the phosphomannomutase genes PMM1, PMM2 and PMM2psi: the sequence variation in the processed pseudogene is a reflection of the mutations found in the functional gene.

The search for the carbohydrate-deficient glycoprotein syndrome type I (CDG1) gene has revealed the existence of a family of phosphomannomutase (PMM) genes in humans. Two expressed PMM genes, PMM1 and PMM2 , are located on chromosome bands 22q13 and 16p13, respectively, and a processed pseudogene PMM2 psi is located on chromosome 18p. Mutations in PMM2 are the cause of CDG type IA whereas no disorder has been associated with defects in PMM1 as yet. Here, we describe the genomic organization of these paralogous genes. There is a 65% identity of the coding sequence, and all intron/exon boundaries have been conserved. The processed pseudogene is more closely related to PMM2 . Remarkably, several base substitutions in PMM2 that are associated with disease are also present at the corresponding positions in the pseudogene. Thus, mutations that occur at a slow rate in the active gene in the population have also accumulated in the pseudogene.

Amino Acid Sequence↗

PubMed2006

Regulation of the homologous two-component systems KvgAS and KvhAS in Klebsiella pneumoniae CG43.

In Klebsiella pneumoniae CG43, deletion of the sensor gene kvgS reduced the kvgAS expression in M9 medium with 0.2 mM paraquat, 0.2 mM 2,2-dihydropyridyl, or 300 mM NaCl. This result shows an autoregulatory role of KvgS and a stress-responsive expression of the two-component system (2CS). The kvgS deletion also appeared to decrease the expression of kvhAS, paralogous genes of kvgAS. Additionally, measurements of the promoter activity in kvgA(-) mutant revealed that KvgA is probably an activator for the expression of kvgAS and kvhAS. The subsequent electrophoretic mobility shift assay, indicating a specific binding of the recombinant KvgA to the putative promoters P(kvgAS) and P(kvhAS), also supported an interacting regulation between the 2CSs. In P(kvgAS) and P(kvhAS), the presence of RpoS binding elements suggested an RpoS-dependent regulation. Nevertheless, the rpoS deletion reduced the expression of kvgAS but increased that of kvhAS. Moreover, the kvgA deletion reduced the expression of katG and sodC. The overexpression of KvhA altered the susceptibility to fosfomycin and an increasing activity of UDP-N-acetylglucosamine enolpyruvyl transferase, the target protein of fosfomycin, which suggesting a regulation by KvhA. Taken together, these indicated that the two 2CSs probably belong to different regulatory circuits of the RpoS regulon.

Amino Acid Sequence↗

PubMed2005

Basal cell nevus syndrome.

PURPOSE OF REVIEW: Basal cell nevus syndrome (BCNS), is a hereditary condition transmitted as an autosomal dominant trait exhibiting high penetrance and variable expressivity. Inherited or spontaneous mutations in the human homologue of the Drosophila patched gene underlie the disorder and in addition to tumor predisposition, are associated with a range of 'patterning' defects. Recent advances, with glimpses of possible therapies are emerging, but because of the wide-ranging nature of phenotypic expression and overlap with other syndromes, there is difficulty. Finally, because of the importance of PTCH and paralogous genes in many species other than humans, reports appear in a correspondingly wide range of journals, which makes 'keeping abreast' difficult. RECENT FINDINGS: Progress has been achieved in understanding the role of Gli-1, 2, & 3 in development of 'sporadic' BCCs and BCNS. Expression of PTCH1 is now known to be regulated by alternative promoters and a single functional Gli-binding site. Expression of FOXE1 as a new transcriptional target of Gli2 has been demonstrated in human epidermis and BCCs. Finally, the discovery of Shh pathway inhibitors such as cyclopamine, a naturally occurring alkaloid and ornithine decarboxylase inhibition suggest possible interventional therapies. SUMMARY: In BCNS, phenotype does not correlate with position of mutations within Patched, suggesting genetic makeup and environment modulate effects of premature protein truncation induced by PTCH mutation. These developmental abnormalities occur as a result of haplo-insufficiency in heterozygotes for the mutated gene, whereas neoplastic complications arise from a classical two-hit tumor suppressor gene model. Attention is therefore turning toward TP53 and PTCH associations.

Animals↗

PubMed2004

Liver invasion by malarial parasites--how do malarial parasites break through the host barrier?

Malarial transmission to the human host is established by sporozoite infection of the liver. Sporozoites are released from the mosquito salivary glands and carried by the blood flow to the liver sinusoid. In the sinusoid, sporozoites leave the blood circulation by crossing the sinusoidal cell layer to infect hepatocytes, the site for their development into the erythrocyte-invasive forms. Traversal of the sinusoidal cell layer and subsequent hepatocyte infection are the most important events in sporozoite liver invasion, but the molecular basis of both events remains to be elucidated. The present review of sporozoite liver invasion focuses on recent advances in this topic obtained by application of reverse genetics. Sporozoites traverse host cells, rupturing the host cell membrane in the process. Three microneme proteins have important roles in this motility. Disruption of one of these genes abolishes or severely impairs cell traversal without affecting other types of invasive motility. Studies using these disruptant parasites indicate that cell-traversal ability is required for crossing the sinusoidal cell layer and accessing the hepatocytes for infection. This process is homologous to midgut epithelium penetration by the malarial ookinete, because identical or paralogous genes are critically involved in both processes. After arrival at the hepatocyte, the invasion mode of the sporozoites switches from cell traversal to hepatocyte infection.

Animals↗

PubMed2025

Avirulence depletion assay: Combining R gene-mediated selection with bulk sequencing for rapid avirulence gene identification in wheat powdery mildew.

Wheat production is threatened by multiple fungal pathogens, such as the wheat powdery mildew fungus (Blumeria graminis f. sp. tritici, Bgt). Wheat resistance breeding frequently relies on the use of resistance (R) genes that encode diverse immune receptors which detect specific avirulence (AVR) effectors and subsequently induce an immune response. While R gene cloning has accelerated recently, AVR identification in many pathogens including Bgt lags behind, preventing pathogen-informed deployment of resistance sources. Here we describe a new "avirulence depletion (AD) assay" for rapid identification of AVR genes in Bgt. This assay relies on the selection of a segregating, haploid F1 progeny population on a resistant host, followed by bulk sequencing, thereby allowing rapid avirulence candidate gene identification with high mapping resolution. In a proof-of-concept experiment we mapped the AVR component of the wheat immune receptor Pm3a to a 25 kb genomic interval in Bgt harboring a single effector, the previously described AvrPm3a2/f2. Subsequently, we applied the AD assay to map the unknown AVR effector recognized by the Pm60 immune receptor. We show that AvrPm60 is encoded by three tandemly arrayed, nearly identical effector genes that trigger an immune response upon co-expression with Pm60 and its alleles Pm60a and Pm60b. We furthermore provide evidence that Pm60 outperforms Pm60a and Pm60b through more efficient recognition of AvrPm60 effectors, suggesting it should be prioritized for wheat breeding. Finally, we show that virulence towards Pm60 is caused by simultaneous deletion of all AvrPm60 gene paralogs and that isolates lacking AvrPm60 are especially prevalent in the US thereby limiting the potential of Pm60 in this region. The AD assay is a powerful new tool for rapid and inexpensive AVR identification in Bgt with the potential to contribute to pathogen-informed breeding decisions for the use of novel R genes and regionally tailored gene deployment.

Triticum↗

PubMed2001

A draft annotation and overview of the human genome.

BACKGROUND: The recent draft assembly of the human genome provides a unified basis for describing genomic structure and function. The draft is sufficiently accurate to provide useful annotation, enabling direct observations of previously inferred biological phenomena. RESULTS: We report here a functionally annotated human gene index placed directly on the genome. The index is based on the integration of public transcript, protein, and mapping information, supplemented with computational prediction. We describe numerous global features of the genome and examine the relationship of various genetic maps with the assembly. In addition, initial sequence analysis reveals highly ordered chromosomal landscapes associated with paralogous gene clusters and distinct functional compartments. Finally, these annotation data were synthesized to produce observations of gene density and number that accord well with historical estimates. Such a global approach had previously been described only for chromosomes 21 and 22, which together account for 2.2% of the genome. CONCLUSIONS: We estimate that the genome contains 65,000-75,000 transcriptional units, with exon sequences comprising 4%. The creation of a comprehensive gene index requires the synthesis of all available computational and experimental evidence.

Chromosome Mapping↗

PubMed2003

Phylogeny of vertebrate nuclear receptors--analysis of variance components in protein sequences.

Nuclear receptors (NR) constitute a large family of proteins and play a crucial role in regulating mineral metabolism and physiological homeostasis of various organ systems. The aim of this study was to elucidate whether the variance among NRs of estrogen, androgen and vitamin-D in various vertebrate species including humans is attributed to differences between the taxonomic groups within a specific receptor (i.e. between orthologous) or between the different proteins within the taxon (i.e. between paralogous genes). Published data on 57 protein sequences of the above NRs were used for phylogenetic analysis. The results showed that in DNA- and ligand-binding regions, 94% and 70% of variance is due to differences between the three proteins. However, in non-binding regions, 47% of the variance results from differences between the three paralogous proteins. Human sequences consistently clustered with their mammal orthologous within the three groups of NR sequences, clearly indicating that evolution of human sequences is not distinct from mammal sequence evolution.

Analysis of Variance↗

PubMed2000

Hox C cluster genes are dispensable for overall body plan of mouse embryonic development.

Hox genes encode transcription factors which provide positional information during morphogenesis along the body axis; genetic interaction among Hox genes is thought to be necessary for correct pattern formation. One of the most curious features of the 39 vertebrate Hox genes is that they form four clusters each composed of several genes paralogous between clusters. This raises the question are all four clusters necessary for the development of vertebrates and, if so, what is the function of each cluster? To provide an answer to this question, we prepared Hox C cluster null mice utilizing the Cre-loxP system. Hox C cluster null mice, lacking all nine Hox C genes, die at the time of birth; however, the mutant pups develop to this stage with minor transformations. This development shows that the Hox C genes are dispensable for the overall body plan of mouse embryogenesis. Furthermore, transformations observed in the skeletal system of the Hox C cluster null mice are milder than those observed in the Hoxc-9 null mice, providing further evidence that at least some genes within a cluster exhibit interaction functions with each other.

Animals↗

PubMed1994

The evolutionary origin of red algae as deduced from the nuclear genes encoding cytosolic and chloroplast glyceraldehyde-3-phosphate dehydrogenases from Chondrus crispus.

Algae are a heterogeneous group of photosynthetic eukaryotes traditionally separated into three major subdivisions: rhodophytes, chlorophytes, and chromophytes. The evolutionary origin of rhodophytes or red algae and their links to other photosynthetic and nonphotosynthetic eukaryotes have been a matter of much controversy and speculation. Here we present the first cDNAs of nuclear protein genes from red algae: Those encoding cytosolic and chloroplast glyceraldehyde-3-phosphate dehydrogenases (GAPDH) from Chondrus crispus. A phylogenetic analysis including GAPDH gene sequences from a number of eukaryotic taxa, cyanobacteria, and purple bacteria suggests that chloroplasts and rhodoplasts together form a monophyletic group of cyanobacterial descent and that rhodophytes separated from chlorophytes at about the same time as animals and fungi. The composite GAPDH tree further demonstrates that chloroplast and cytosolic GAPDH genes are closely related to their homologs in cyanobacteria and purple bacteria, respectively, the presumptive ancestors of chloroplasts and mitochondria, thereby firmly establishing the endosymbiotic origin of these nuclear genes and their fixation in eukaryotic cells before the rhodophyte/chlorophyte separation. The present data are in conflict with phylogenetic inferences based on plastid-encoded rbcL sequences supporting a polyphyletic origin of rhodoplasts and chloroplasts. Comparison of rbcL to GAPDH phylogenies suggests that rbcL trees may be misleading because they are composed of branches representing ancient duplicated (paralogous) genes.

Amino Acid Sequence↗

PubMed2025

Loss and Gain of Aqp10 Paralogs With Broad Solute Selectivity in Anguillid Eels.

Aquaporin (Aqp) 10 is a member of the aquaglyceriporin family, which transports small, uncharged solutes in addition to water. Although the solute selectivity of aquaglyceroporins varies, the mechanism of solute selectivity has not yet been fully elucidated. The common ancestor of ray-finned fish possessed two paralogous genes for aquaporin 10, aqp10.1 and aqp10.2, which produce Aqps with different solute selectivities. Most teleosts possess one or more ohnologs derived from aqp10.1 and aqp10.2; however, the common ancestor of Anguilliformes species lost all aqp10.1-derived ohnologs. Anguilliformes species, except Anguilla species, have one aqp10.2b, but recent tandem duplications in the European eel have generated three aqp10.2b paralogs (aqp10.2b1-aqp10.2b3), whose activities remain ambiguous. In this study, we found that the four sites forming the aromatic/arginine (ar/R) selectivity filter in European eel Aqp10.2b1 were identical to those in Aqp10.2b of other species. However, the Y residue at position 3 was replaced with G in the ar/R selectivity filter of Aqp10.2b2 and b3. When expressed in Xenopus oocytes, Aqp10.2b2 and b3 showed higher permeability to urea and boric acid than Aqp10.2b1, indicating that Aqp10.2b2 and b3 acquired broad solute selectivity similar to that of Aqp10.1, which was lost in the ancestral Anguilliformes species. Urea and boric acid permeabilities of Aqp10.2b1 increased when the Y residue at position 3 of the ar/R selectivity filter was replaced with G. Overall, our results outline the history of the loss and gain of Aqp10 paralogs with broad solute selectivity in anguillid eels.

Animals↗

PubMed2003

Tropheryma whipplei Twist: a human pathogenic Actinobacteria with a reduced genome.

The human pathogen Tropheryma whipplei is the only known reduced genome species (<1 Mb) within the Actinobacteria [high G+C Gram-positive bacteria]. We present the sequence of the 927303-bp circular genome of T. whipplei Twist strain, encoding 808 predicted protein-coding genes. Specific genome features include deficiencies in amino acid metabolisms, the lack of clear thioredoxin and thioredoxin reductase homologs, and a mutation in DNA gyrase predicting a resistance to quinolone antibiotics. Moreover, the alignment of the two available T. whipplei genome sequences (Twist vs. TW08/27) revealed a large chromosomal inversion the extremities of which are located within two paralogous genes. These genes belong to a large cell-surface protein family defined by the presence of a common repeat highly conserved at the nucleotide level. The repeats appear to trigger frequent genome rearrangements in T. whipplei, potentially resulting in the expression of different subsets of cell surface proteins. This might represent a new mechanism for evading host defenses. The T. whipplei genome sequence was also compared to other reduced bacterial genomes to examine the generality of previously detected features. The analysis of the genome sequence of this previously largely unknown human pathogen is now guiding the development of molecular diagnostic tools and more convenient culture conditions.

Actinomycetales↗