A Cluster of Cuticle Protein Genes of Drosophila melanogaster at 65A: Sequence, Structure and Evolution

A 36-kb genomic DNA segment of the Drosophila melanogaster genome containing 12 clustered cuticle genes has been mapped and partially sequenced. The cluster maps at 65A 5-6 on the left arm of the third chromosome, in agreement with the previously determined location of a putative cluster encompassing the genes for the third instar larval cuticle proteins LCP5, LCP6 and LCP8. This cluster is the largest cuticle gene cluster discovered to date and shows a number of surprising features that explain in part the genetic complexity of the LCP5, LCP6 and LCP8 loci. The genes encoding LCP5 and LCP8 are multiple copy genes and the presence of extensive similarity in their coding regions gives the first evidence for gene conversion in cuticle genes. In addition, five genes in the cluster are intronless. Four of these five have arisen by retroposition. The other genes in the cluster have a single intron located at an unusual location for insect cuticle genes.

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Functional genomic analysis of the 61D-61F region of the third chromosome of Drosophila melanogaster

Genome ◽

10.1139/g03-081 ◽

2003 ◽

Vol 46 (6) ◽

pp. 1049-1058 ◽

Cited By ~ 7

Author(s):

Ho-Chun Wei ◽

Huidy Shu ◽

James V Price

Keyword(s):

Drosophila Melanogaster ◽

Genomic Sequence ◽

Genomic Analysis ◽

Porphobilinogen Deaminase ◽

The Third ◽

Physical Maps ◽

Functional Genomic Analysis ◽

Genes Encoding ◽

Complementation Groups ◽

Genomic Contig

Assigning functional significance to completed genome sequences is one of the next challenges in biological science. Conventional genetic tools such as deficiency chromosomes help assign essential complementation groups to their corresponding genes. We describe an F2 genetic screen to identify lethal mutations within cytogenetic region 61D-61F of the third chromosome of Drosophila melanogaster. One hundred sixteen mutations were identified by their failure to complement both Df(3L)bab-PG and Df(3L)3C7. These alleles were assigned to 14 complementation groups and 9 deficiency intervals. Complementation groups were ordered using existing deficiencies, as well as new deficiencies generated in this study. With the aid of the genomic sequence, genetic and physical maps in the region were correlated by use of PCR to localize the breakpoints of deficiencies within a 268-kb genomic contig (GenBank accession No. AC005847). Six essential complementation groups were assigned to specific genes, including genes encoding a porphobilinogen deaminase and a Sac1-like protein.Key words: Drosophila, functional genomics, porphobilinogen deaminase, synaptojanin.

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Cuticle protein gene expression during the third instar of Drosophila melanogaster

Insect Biochemistry ◽

10.1016/0020-1790(88)90087-x ◽

1988 ◽

Vol 18 (3) ◽

pp. 229-235 ◽

Cited By ~ 17

Author(s):

Deborah A. Kimbrell ◽

Edward Berger ◽

David S. King ◽

William J. Wolfgang ◽

James W. Fristrom

Keyword(s):

Gene Expression ◽

Drosophila Melanogaster ◽

Protein Gene ◽

The Third ◽

Cuticle Protein

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THE CUTICLE PROTEINS OF DROSOPHILA MELANOGASTER: GENETIC LOCALIZATION OF A SECOND CLUSTER OF THIRD-INSTAR GENES

Genetics ◽

10.1093/genetics/114.2.393 ◽

1986 ◽

Vol 114 (2) ◽

pp. 393-404

Author(s):

Carol J Chihara ◽

Deborah A Kimbrell

Keyword(s):

Recessive Mutation ◽

Larval Cuticle ◽

Gene Map ◽

The Third ◽

Naturally Occurring ◽

Induced Mutants ◽

Recessive Mutant ◽

Cuticle Protein ◽

Cuticle Proteins ◽

New Protein

ABSTRACT Five third-instar larval cuticle protein genes are placed on the left arm of the third chromosome. For these five genes, 12 variants and two induced mutants are described. All the naturally occurring variants are codominant. One EMS-induced mutant is characterized by the codominant appearance of a new protein, and a second by a recessive mutation that codes for a modifier of third-instar larval cuticle protein 5 (L3CP-5). All but the putative modifier gene map to within less than 0.3 map units of each other on the left arm of the third chromosome at approximately 11. We propose that these genes constitute a cluster of third-instar cuticle protein genes. The induced recessive mutant maps outside of the cluster to a region also on the left arm of the third chromosome. The proteins and their genes should prove useful for both developmental and evolutionary studies.

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GENETIC AND BIOCHEMICAL BASIS OF ENZYME ACTIVITY VARIATION IN NATURAL POPULATIONS. I. ALCOHOL DEHYDROGENASE IN DROSOPHILA MELANOGASTER

Genetics ◽

10.1093/genetics/89.2.371 ◽

1978 ◽

Vol 89 (2) ◽

pp. 371-388

Author(s):

John F McDonald ◽

Francisco J Ayala

Keyword(s):

Gene Regulation ◽

Drosophila Melanogaster ◽

Alcohol Dehydrogenase ◽

Natural Populations ◽

Difficult Problem ◽

Regulatory Genes ◽

Biochemical Basis ◽

Evolutionary Consequence ◽

The Third ◽

Adh Activity

ABSTRACT Recent studies by various authors suggest that variation in gene regulation may be common in nature, and might be of great evolutionary consequence; but the ascertainment of variation in gene regulation has proven to be a difficult problem. In this study, we explore this problem by measuring alcohol dehydrogenase (ADH) activity in Drosophila melanogaster strains homozygous for various combinations of given second and third chromosomes sampled from a natural population. The structural locus (Adh) coding for ADH is on the second chromosome. The results show that: (1) there are genes, other than Adh, that affect the levels of ADH activity; (2) at least some of these "regulatory" genes are located on the third chromosome, and thus are not adjacent to the Adh locus; (3) variation exists in natural populations for such regulatory genes; (4) the effect of these regulatory genes varies as they interact with different second chromosomes; (5) third chromosomes with high-activity genes are either partially or completely dominant over chromosomes with low-activity genes; (6) the effects of the regulatory genes are pervasive throughout development; and (7) the third chromosome genes regulate the levels of ADH activity by affecting the number of ADH molecules in the flies. The results are consistent with the view that the evolution of regulatory genes may play an important role in adaptation.

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Phenotypic interactions of spinster with the genes encoding proteins for cell death control in Drosophila melanogaster

Archives of Insect Biochemistry and Physiology ◽

10.1002/arch.20345 ◽

2010 ◽

Vol 73 (3) ◽

pp. 119-127 ◽

Cited By ~ 5

Author(s):

Akira Sakurai ◽

Yoshiro Nakano ◽

Masayuki Koganezawa ◽

Daisuke Yamamoto

Keyword(s):

Cell Death ◽

Drosophila Melanogaster ◽

Genes Encoding

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Molecular Evolution of Duplicated Amylase Gene Regions in Drosophila melanogaster: Evidence of Positive Selection in the Coding Regions and Selective Constraints in the cis-Regulatory Regions

Genetics ◽

10.1093/genetics/157.2.667 ◽

2001 ◽

Vol 157 (2) ◽

pp. 667-677

Author(s):

Hitoshi Araki ◽

Nobuyuki Inomata ◽

Tsuneyuki Yamazaki

Keyword(s):

Drosophila Melanogaster ◽

Molecular Evolution ◽

Positive Selection ◽

Natural Populations ◽

Sliding Window ◽

Selective Constraint ◽

Proximal Region ◽

Coding Regions ◽

Asian Populations ◽

Flanking Region

Abstract In this study, we randomly sampled Drosophila melanogaster from Japanese and Kenyan natural populations. We sequenced duplicated (proximal and distal) Amy gene regions to test whether the patterns of polymorphism were consistent with neutral molecular evolution. Fst between the two geographically distant populations, estimated from Amy gene regions, was 0.084, smaller than reported values for other loci, comparing African and Asian populations. Furthermore, little genetic differentiation was found at a microsatellite locus (DROYANETSB) in these samples (Gst′=−0.018). The results of several tests (Tajima's, Fu and Li's, and Wall's tests) were not significantly different from neutrality. However, a significantly higher level of fixed replacement substitutions was detected by a modified McDonald and Kreitman test for both populations. This indicates that positive selection occurred during or immediately after the speciation of D. melanogaster. Sliding-window analysis showed that the proximal region 1, a part of the proximal 5′ flanking region, was conserved between D. melanogaster and its sibling species, D. simulans. An HKA test was significant when the proximal region 1 was compared with the 5′ flanking region of Alcohol dehydrogenase (Adh), indicating a severe selective constraint on the Amy proximal region 1. These results suggest that natural selection has played an important role in the molecular evolution of Amy gene regions in D. melanogaster.

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A Family of Genes Clustered at the Triplo-lethal Locus of Drosophila melanogaster Has an Unusual Evolutionary History and Significant Synteny With Anopheles gambiae

Genetics ◽

10.1093/genetics/165.2.613 ◽

2003 ◽

Vol 165 (2) ◽

pp. 613-621 ◽

Cited By ~ 2

Author(s):

Douglas R Dorer ◽

Jamie A Rudnick ◽

Etsuko N Moriyama ◽

Alan C Christensen

Keyword(s):

Phylogenetic Analysis ◽

Drosophila Melanogaster ◽

Anopheles Gambiae ◽

Evolutionary History ◽

Codon Bias ◽

Good Target ◽

The Family ◽

Genes Encoding ◽

And Function ◽

Gambiae Genome

Abstract Within the unique Triplo-lethal region (Tpl) of the Drosophila melanogaster genome we have found a cluster of 20 genes encoding a novel family of proteins. This family is also present in the Anopheles gambiae genome and displays remarkable synteny and sequence conservation with the Drosophila cluster. The family is also present in the sequenced genome of D. pseudoobscura, and homologs have been found in Aedes aegypti mosquitoes and in four other insect orders, but it is not present in the sequenced genome of any noninsect species. Phylogenetic analysis suggests that the cluster evolved prior to the divergence of Drosophila and Anopheles (250 MYA) and has been highly conserved since. The ratio of synonymous to nonsynonymous substitutions and the high codon bias suggest that there has been selection on this family both for expression level and function. We hypothesize that this gene family is Tpl, name it the Osiris family, and consider possible functions. We also predict that this family of proteins, due to the unique dosage sensitivity and the lack of homologs in noninsect species, would be a good target for genetic engineering or novel insecticides.

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The clp1 Gene of the Mushroom Coprinus cinereus Is Essential for A-Regulated Sexual Development

Genetics ◽

10.1093/genetics/157.1.133 ◽

2001 ◽

Vol 157 (1) ◽

pp. 133-140

Author(s):

Kazumi Inada ◽

Yoshinori Morimoto ◽

Toshihide Arima ◽

Yukio Murata ◽

Takashi Kamada

Keyword(s):

Sexual Development ◽

Genomic Dna ◽

Mutant Allele ◽

Coprinus Cinereus ◽

Mating Partner ◽

Essential Step ◽

Genes Encoding ◽

Dna Fragment ◽

Necessary And Sufficient ◽

Novel Protein

Abstract Sexual development in the mushroom Coprinus cinereus is under the control of the A and B mating-type loci, both of which must be different for a compatible, dikaryotic mycelium to form between two parents. The A genes, encoding proteins with homeodomain motifs, regulate conjugate division of the two nuclei from each mating partner and promote the formation of clamp connections. The latter are hyphal configurations required for the maintenance of the nuclear status in the dikaryotic phase of basidiomycetes. The B genes encode pheromones and pheromone receptors. They regulate the cellular fusions that complete clamp connections during growth, as well as the nuclear migration required for dikaryosis. The AmutBmut strain (326) of C. cinereus, in which both A- and B-regulated pathways are constitutively activated by mutations, produces, without mating, dikaryon-like, fertile hyphae with clamp connections. In this study we isolated and characterized clampless1-1 (clp1-1), a mutation that blocks clamp formation, an essential step in A-regulated sexual development, in the AmutBmut background. A genomic DNA fragment that rescues the clp1-1 mutation was identified by transformations. Sequencing of the genomic DNA, together with RACE experiments, identified an ORF interrupted by one intron, encoding a novel protein of 365 amino acids. The clp1-1 mutant allele carries a deletion of four nucleotides, which is predicted to cause elimination of codon 128 and frameshifts thereafter. The clp1 transcript was normally detected only in the presence of the A protein heterodimer formed when homokaryons with compatible A genes were mated. Forced expression of clp1 by promoter replacements induced clamp development without the need for a compatible A gene combination. These results indicate that expression of clp1 is necessary and sufficient for induction of the A-regulated pathway that leads to clamp development.

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Identification and Characterization of the Genes Encoding the Core Histones and Histone Variants of Neurospora crassa

Genetics ◽

10.1093/genetics/160.3.961 ◽

2002 ◽

Vol 160 (3) ◽

pp. 961-973 ◽

Cited By ~ 1

Author(s):

Shan M Hays ◽

Johanna Swanson ◽

Eric U Selker

Keyword(s):

Neurospora Crassa ◽

Histone Variants ◽

Null Alleles ◽

Histone Genes ◽

Histone H4 ◽

Coding Regions ◽

The Core ◽

Genomic Arrangement ◽

Genes Encoding ◽

Core Histones

Abstract We have identified and characterized the complete complement of genes encoding the core histones of Neurospora crassa. In addition to the previously identified pair of genes that encode histones H3 and H4 (hH3 and hH4-1), we identified a second histone H4 gene (hH4-2), a divergently transcribed pair of genes that encode H2A and H2B (hH2A and hH2B), a homolog of the F/Z family of H2A variants (hH2Az), a homolog of the H3 variant CSE4 from Saccharomyces cerevisiae (hH3v), and a highly diverged H4 variant (hH4v) not described in other species. The hH4-1 and hH4-2 genes, which are 96% identical in their coding regions and encode identical proteins, were inactivated independently. Strains with inactivating mutations in either gene were phenotypically wild type, in terms of growth rates and fertility, but the double mutants were inviable. As expected, we were unable to isolate null alleles of hH2A, hH2B, or hH3. The genomic arrangement of the histone and histone variant genes was determined. hH2Az and the hH3-hH4-1 gene pair are on LG IIR, with hH2Az centromere-proximal to hH3-hH4-1 and hH3 centromere-proximal to hH4-1. hH3v and hH4-2 are on LG IIIR with hH3v centromere-proximal to hH4-2. hH4v is on LG IVR and the hH2A-hH2B pair is located immediately right of the LG VII centromere, with hH2A centromere-proximal to hH2B. Except for the centromere-distal gene in the pairs, all of the histone genes are transcribed toward the centromere. Phylogenetic analysis of the N. crassa histone genes places them in the Euascomycota lineage. In contrast to the general case in eukaryotes, histone genes in euascomycetes are few in number and contain introns. This may be a reflection of the evolution of the RIP (repeat-induced point mutation) and MIP (methylation induced premeiotically) processes that detect sizable duplications and silence associated genes.

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