Identification of cfxR, an activator gene of autotrophic CO2 fixation in Alcaligenes eutrophus

A regulatory gene, cfxR, involved in the carbon dioxide assimilation of Alcaligenes eutrophus H16 has been characterized through the analysis of mutants. The function of cfxR is required for the expression of two cfx operons that comprise structural genes encoding Calvin cycle enzymes. CfxR (34.8 kDa) corresponds with an open reading frame of 954 bp, with a translational initiation codon 167 bp upstream of the chromosomal cfx operon. The cfx operon and cfxR are transcribed divergently. The N-terminal sequence of CfxR is very similar to those of bacterial regulatory proteins belonging to the LysR family. Heterologous expression of cfxR in Escherichia coli was achieved using the pT7-7 system. Mobility shift experiments demonstrated that CfxR is a DNA-binding protein with a target site upstream of both the chromosomal and the plasmid-encoded cfx operons.     

Cloning and expression of chromosomally and plasmid-encoded glyceraldehyde-3-phosphate dehydrogenase genes from the chemoautotroph Alcaligenes eutrophys

Abstract Hybridizations using heterologous glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene probes suggested the existence of three GAPDH genes in Alcaligenes eutrophus H16. Two of these, located on the chromosome and the megaplasmid pHG1 of the organism, respectively, mapped about 2.5 kilobase pairs (kb) downstream of the two duplicated CO₂ fixation gene clusters ( cfx genes). They were identified as GAPDH genes ( cfxG _c and cfxG _p ) by cloning and expression in Escherichia coli . These genes encode GAPDH isoenzymes functioning in the Calvin cycle. The third gene ( gap ) is chromosomally encoded but not linked to the cfx _c cluster. Its product is probably involved in heterotrophic carbon metabolism.     

The Calvin cycle enzyme pentose-5-phosphate 3-epimerase is encoded within the cfx operons of the chemoautotroph Alcaligenes eutrophus.

Several genes (cfx genes) encoding Calvin cycle enzymes in Alcaligenes eutrophus are organized in two highly homologous operons comprising at least 11 kb. One cfx operon is located on the chromosome; the other is located on megaplasmid pHG1 of the organism (B. Bowien, U. Windh?vel, J.-G. Yoo, R. Bednarski, and B. Kusian, FEMS Microbiol. Rev. 87:445-450, 1990). Corresponding regions of about 2.7 kb from within the operons were sequenced. Three open reading frames, designated cfxX (954 bp), cfxY (765 bp), and cfxE (726 bp), were detected at equivalent positions in the two sequences. The nucleotide identity of the sequences amounted to 94%. Heterologous expression of the subcloned pHG1-encoded open reading frames in Escherichia coli suggested that they were functional genes. The observed sizes of the gene products CfxX (35 kDa), CfxY (27 kDa), and CfxE (25.5 kDa) closely corresponded to the values calculated on the basis of the sequence information. E. coli clones harboring the cfxE gene showed up to about 19-fold-higher activities of pentose-5-phosphate 3-epimerase (PPE; EC 5.1.3.1) than did reference clones, suggesting that cfxE encodes PPE, another Calvin cycle enzyme. These data agree with the finding that in A. eutrophus, PPE activity is significantly enhanced under autotrophic growth conditions which lead to a derepression of the cfx operons. No functions could be assigned to CfxX and CfxY.     

Differential regulation of ParaHox genes by retinoic acid in the invertebrate chordate amphioxus (Branchiostoma floridae)

The ParaHox cluster is the evolutionary sister to the Hox cluster. Like the Hox cluster, the ParaHox cluster displays spatial and temporal regulation of the component genes along the anterior/posterior axis in a manner that correlates with the gene positions within the cluster (a feature called collinearity). The ParaHox cluster is however a simpler system to study because it is composed of only three genes. We provide a detailed analysis of the amphioxus ParaHox cluster and, for the first time in a single species, examine the regulation of the cluster in response to a single developmental signalling molecule, retinoic acid (RA). Embryos treated with either RA or RA antagonist display altered ParaHox gene expression: AmphiGsx expression shifts in the neural tube, and the endodermal boundary between AmphiXlox and AmphiCdx shifts its anterior/posterior position. We identified several putative retinoic acid response elements and in vitro assays suggest some may participate in RA regulation of the ParaHox genes. By comparison to vertebrate ParaHox gene regulation we explore the evolutionary implications. This work highlights how insights into the regulation and evolution of more complex vertebrate arrangements can be obtained through studies of a simpler, unduplicated amphioxus gene cluster.     

Genes encoding cuticular proteins are components of the Nimrod gene cluster in Drosophila

The Nimrod gene cluster, located on the second chromosome of Drosophila melanogaster, is the largest synthenic unit of the Drosophila genome. Nimrod genes show blood cell specific expression and code for phagocytosis receptors that play a major role in fruit fly innate immune functions. We previously identified three homologous genes (vajk-1, vajk-2 and vajk-3) located within the Nimrod cluster, which are unrelated to the Nimrod genes, but are homologous to a fourth gene (vajk-4) located outside the cluster. Here we show that, unlike the Nimrod candidates, the Vajk proteins are expressed in cuticular structures of the late embryo and the late pupa, indicating that they contribute to cuticular barrier functions.     

A conserved gene cluster as a putative functional unit in insect innate immunity

The Nimrod gene superfamily is an important component of the innate immune response. The majority of its member genes are located in close proximity within the Drosophila melanogaster genome and they lie in a larger conserved cluster (“Nimrod cluster”), made up of non-related groups (families, superfamilies) of genes. This cluster has been a part of the Arthropod genomes for about 300-350 million years. The available data suggest that the Nimrod cluster is a functional module of the insect innate immune response.     

Evolution of the CYP2ABFGST gene cluster in rat, and a fine-scale comparison among rodent and primate species

The evolution of gene families can be best understood by studying the modern organization and functions of family members, and by comparing parallel families in different species. In this study, the CYP2ABFGST gene cluster has been characterized in rat and compared to the syntenic clusters in mouse and human, providing an interesting example of gene family evolution. In the rat, 18 loci from six subfamilies have been identified by specifically amplifying and sequencing gene fragments from cloned DNA, and have been exactly placed on chromosome 1. The overall organization of the gene cluster in rat is relatively simple, with genes from each subfamily in tandem, and is more similar to the mouse than to the human cluster. We have reconstructed the probable structure of the CYP2ABFGST cluster in the common ancestor of primates and rodents, and inferred a model of the evolution of this gene cluster in the three species. Numerous nontandem and block duplications, inversions, and translocations have occurred entirely inside the cluster, indicating that pairing between duplicate genes is keeping the rearrangements within the cluster region. The initial tandem duplication of a CYP2 gene in an early mammalian ancestor has made this region particularly subject to such localized rearrangements. Even if duplicated genes do not have a large-scale effect on chromosomal rearrangements, on a local level clustered gene families may have contributed significantly to the genomic complexity of modern mammals.     

Distribution of gibberellin biosynthetic genes and gibberellin production in the Gibberella fujikuroi species complex

Gibberella fujikuroi is a species-rich monophyletic complex of at least nine sexually fertile biological species (mating populations, MP-A to MP-I) and more than 30 anamorphs in the genus Fusarium. They produce a variety of secondary metabolites, such as fumonisins, fusaproliferin, moniliformin, beauvericin, fusaric acid, and gibberellins (GAs), a group of plant hormones. In this study, we examined for the first time all nine sexually fertile species (MPs) and additional anamorphs within and outside the G. fujikuroi species complex for the presence of GA biosynthetic genes. So far, the ability to produce GAs was described only for Fusarium fujikuroi (G. fujikuroi MP-C), which contains seven clustered genes in the genome all participating in GA biosynthesis. We show that six other MPs (MPs B, D, E, F, G, and I) and most of the anamorphs within the species complex also contain the entire gene cluster, except for F. verticillioides (MP-A), and F. circinatum (MP-H), containing only parts of it. Despite the presence of the entire gene cluster in most of the species within the G. fujikuroi species complex, expression of GA biosynthetic genes and GA production were detected only in F. fujikuroi (MP-C) and one isolate of F. konzum (MP-I). We used two new molecular marker genes, P450-4 from the GA gene cluster, and cpr, encoding the highly conserved NADPH cytochrome P450 reductase to study phylogenetic relationships within the G. fujikuroi species complex. The molecular phylogenetic studies for both genes have revealed good agreement with phylogenetic trees inferred from other genes. Furthermore, we discuss the role and evolutionary origin of the GA biosynthetic gene cluster.     

Identifying subset of genes that have influential impacts on cancer progression: a new approach to analyze cancer microarray data

Cancer is a complex genetic disease, resulting from defects of multiple genes. Development of microarray techniques makes it possible to survey the whole genome and detect genes that have influential impacts on the progression of cancer. Statistical analysis of cancer microarray data is challenging because of the high dimensionality and cluster nature of gene expressions. Here, clusters are composed of genes with coordinated pathological functions and/or correlated expressions. In this article, we consider cancer studies where censored survival endpoint is measured along with microarray gene expressions. We propose a hybrid clustering approach, which uses both pathological pathway information retrieved from KEGG and statistical correlations of gene expressions, to construct gene clusters. Cancer survival time is modeled as a linear function of gene expressions. We adopt the clustering threshold gradient directed regularization (CTGDR) method for simultaneous gene cluster selection, within-cluster gene selection, and predictive model building. Analysis of two lymphoma studies shows that the proposed approach - which is composed of the hybrid gene clustering, linear regression model for survival, and clustering regularized estimation with CTGDR - can effectively identify gene clusters and genes within selected clusters that have satisfactory predictive power for censored cancer survival outcomes.     

Evolution of Growth Hormone in Primates: The GH Gene Clusters of the New World Monkeys Marmoset (Callithrix jacchus) and White-Fronted Capuchin (Cebus albifrons)

The GH gene cluster in marmoset, Callithrix jacchus, comprises eight GH-like genes and pseudogenes and appears to have arisen as a consequence of gene duplications occurring independently of those leading to the human GH gene cluster. We report here the complete sequence of the marmoset GH gene locus, including the intergenic regions and 5′ and 3′ flanking sequence, and a study of the multiple GH-like genes of an additional New World monkey (NWM), the white-fronted capuchin, Cebus albifrons. The marmoset sequence includes 945 nucleotides (nt) of 5′ flanking sequence and 1596 nt of 3′ flanking sequence that are “unique”; between these are eight repeat units, including the eight GH genes/pseudogenes. The breakpoints between these repeats are very similar, indicating a regular pattern of gene duplication. These breakpoints do not correspond to those found in the much less regular human GH gene cluster. This and phylogenetic analysis of the repeat units within the marmoset gene cluster strongly support the independent origin of these gene clusters, and the idea that the episode of rapid evolution that occurred during GH evolution in primates preceded the gene duplications. The marmoset GH gene cluster also differs from that of human in having fewer and more evenly distributed Alu sequences (a single pair in each repeat unit) and a “P-element” upstream of every gene/pseudogene. In human there is no P-element upstream of the gene encoding pituitary GH, and these elements have been implicated in placental expression of the other genes of the cluster. The GH gene clusters in marmoset and capuchin appear to have arisen as the consequence of a single-gene duplication event, but in capuchin there was then a remarkable expansion of the GH locus, giving at least 40 GH-like genes and pseudogenes. Thus even among NWMs the GH gene cluster is very variable. [Reviewing Editor: Nicolas Galtier]     

Comprehensive analysis of keratin gene clusters in humans and rodents

Here, we present the comparative analysis of the two keratin (K) gene clusters in the genomes of man, mouse and rat. Overall, there is a remarkable but not perfect synteny among the clusters of the three mammalian species. The human type I keratin gene cluster consists of 27 genes and 4 pseudogenes, all in the same orientation. It is interrupted by a domain of multiple genes encoding keratin-associated proteins (KAPs). Cytokeratin, hair and inner root sheath keratin genes are grouped together in small subclusters, indicating that evolution occurred by duplication events. At the end of the rodent type I gene cluster, a novel gene related to K14 and K17 was identified, which is converted to a pseudogene in humans. The human type II cluster consists of 27 genes and 5 pseudogenes, most of which are arranged in the same orientation. Of the 26 type II murine keratin genes now known, the expression of two new genes was identified by RT-PCR. Kb20, the first gene in the cluster, was detected in lung tissue. Kb39, a new ortholog of K1, is expressed in certain stratified epithelia. It represents a candidate gene for those hyperkeratotic skin syndromes in which no K1 mutations were identified so far. Most remarkably, the human K3 gene which causes Meesmann's corneal dystrophy when mutated, lacks a counterpart in the mouse genome. While the human genome has 138 pseudogenes related to K8 and K18, the mouse and rat genomes contain only 4 and 6 such pseudogenes. Our results also provide the basis for a unified keratin nomenclature and for future functional studies.     

A fragmented aflatoxin-like gene cluster in the forest pathogen Dothistroma septosporum

The polyketide toxin dothistromin is very similar in structure to the aflatoxin precursor, versicolorin B. Dothistromin is made by a pine needle pathogen, Dothistroma septosporum, both in culture and in planta. Orthologs of aflatoxin biosynthetic genes have been identified that are required for dothistromin biosynthesis in D. septosporum. In contrast to the situation in aflatoxin-producing fungi where 25 aflatoxin biosynthetic and regulatory genes are tightly clustered in one region of the genome, the dothistromin gene cluster is fragmented. Three mini-clusters of dothistromin genes have been identified, each located on a 1.3-Mb chromosome and each grouped with non-dothistromin genes. There are no obvious patterns of repeated sequences or transposon relics to suggest recent recombination events. Most dothistromin genes within the mini-clusters are co-regulated, suggesting that coordinate control of gene expression is achieved despite this unusual arrangement of secondary metabolite biosynthetic genes.     

The genomic organization and evolution of the natural killer immunoglobulin-like receptor (KIR) gene cluster

Natural killer (NK) immunoglobulin-like receptors (KIRs) are a family of polymorphic receptors which interact with specific motifs on HLA class I molecules and modulate NK cytolytic activity. In this study, we analyzed a recently sequenced subgenomic region on chromosome 19q13.4 containing eight members of the KIR receptor repertoire. Six members are clustered within a 100-kb continuous sequence. These genes include a previously unpublished member of the KIR gene family 2DS6, as well as 2DL1, 2DL4, 3DL1, 2DS4, 3DL2, from centromere to telomere. Two additional KIR genes, KIRCI and 2DL3, which may be located centromeric of this cluster were also analyzed. We show that the KIR genes have undergone repeated gene duplications. Diversification between the genes has occurred postduplication primarily as a result of retroelement indels and gene truncation. Using pre- and postduplication Alu sequences identified within these genes as evolutionary molecular clocks, the evolution and duplication of this gene cluster is estimated to have occurred 30–45 million years ago, during primate evolution. A proposed model of the duplication history of the KIR gene family leading to their present organization is presented. Received: 25 November 1999 / Revised: 10 January 2000