Drosophila Genome and its Life Cycle

SUBHRADEEP SARKARM.Sc IN APPLIED GENETICS

A wild-type Drosophila melanogaster, or fruit fly, has multifaceted brick red eyes, a tan thorax studded with arched black bristles, a striped abdomen, and a pair of translucent wings.

The fly’s rapid life cycle, low chromosome number, small genome size, and giant salivary gland chromosomes are among the experimentaladvantages that made D. melanogaster the central organism in the study of transmission genetics in the first half of the twentieth century.

These same features also made Drosophila a major model organism in genetic studies of animal development and behavior in the last quarter of the century.

Why is so much attention paid to Drosophila genome?

61 % human diseases have recognizable correspondence in genetic code of fruit fly

50 % of protein sequences have analogs with mammals

Drosophila is

used in genetic simulations of some human diseases, including Parkinson's disease, Alzheimer's sclerosis and disease of Hantington

used for exploration of mechanisms laid in the basis of immunity, diabetes, cancer and narcotic dependence

model system for the investigation of many developmental and cellular processes common to higher eukaryotes, including humans

Drosophila and human development are homologous processes. Unlike humans, Drosophila is subject to easy genetic manipulation. As a result, most of what we know about the molecular basis of animal development has come from studies of model systems such as Drosophila.

Modern Drosophila genetics originated with Thomas Hunt Morgan’s discovery of the sex-linked white eye mutation in 1910.

The fountainhead of Drosophila genetics. Thomas Hunt Mor-gan and his students in the fly room at Columbia University, at a party in 1919. Morgan (back row, far left), Sturtevant (front row, third from the right), Calvin Bridges (back row, third from the right), and Herman J. Muller (back row, second from the left).

Giant polytene chromosomes of larval salivary gland are key tools Replicate 10-11 times 1024-2048 sister chromatids

stay associated under perfect lateral register

Homologous chromosome stay tightly synapsed

Chromocenter – common region where centromeres coalesce

Fig. 14.6a

Several characteristics of Drosophila are useful forgenetic analysis.a. The life cycle is relatively short, and each fly canproduce thousands of progeny.b. A moderate amount of crossing-over occurs infemales and no crossing-over occurs in males.c. Balancer chromosomes help preserve linkage.d. P-element transposons are tools of molecularmanipulation useful for transformation, genetagging, and enhancer trapping.e. Genetic mosaics resulting from mitotic recombinationhelp track the roles of individual genes in the development of specific body structures.f. Ectopic expression can help pin down the function of a gene by making it possible to examine the effects of overexpressing the gene product or expressing the gene product in the wrong tissues.

Genetic regulation of development in Drosophila:

Fig. 19.18,

Developmental stages of Drosophila(10-12 days)

Egg

Larva (3 instars)

Pupa

Adult

Structure of the Drosophila Genome Chromosomes of

Drosophila Four chromosomes

designated 1-4 XY sex

determination (XX females, XY males)

Sex determined by X:A ratio

Structure and Organization of the

Drosophila Genome

The Drosophila genome is about 5% the size of the humangenome and is packaged in far fewer chromosomes.

It contains roughly 13,600 genes, about a half of the number found in the human genome.

This means that the density of genes on Drosophila chromosomes is higher than that of genes in the human genome. Even so, about one-third of the fly genome consists of repetitive sequences that do not encode proteins or that act as transposable elements.

Drosophila GenomeThe haploid genome contains about 170,000 kb of DNA.Roughly 21% of this DNA consists of highly repetitive“satellite” DNA that is concentrated in the centromericheterochromatin and the Y chromosome.

Another 3% consists of repeated genes that encode rRNA, 5S RNA, and the histone proteins

Approximately 9% is composed of around 50 families of transposable elements, which are roughly 2–9 kb in length; the number of copies of each type of element varies from strain to strain but is usually somewhere between 10 and 100.

In addition to residing at scatteredsites within the euchromatin, many transposable elementsare found in the centromeric heterochromatin, while someare concentrated in telomeres.

An unusual feature of Drosophila chromosomes is that the telomeres do not consist of simple repeats, such as the TTGGGG or TTAGGG repeats found at the ends of chromosomes in other well characterized organisms.

Instead, it appears that the rapid jumping into the telomeric region of certain kinds of transposable elements maintains the telomeres.

These insertions into the telomeric region of the transposable elements counter the chromosomal shortening that inevitably occurs during the replication of the ends of linear DNA molecules.

The remaining 67% of the genome consists of unique DNA sequences that reside mostly in the euchromatic arms.

The Drosophila Genome Project has already sequenced the euchromatic portion of the genome.

Analysis of this sequence suggests that there areapproximately 13,600 genes in the fly genome.

A major remaining goal of the Drosophila Genome Projectis to obtain information about the function of each ofthese genes. Large collections of transposon-induced mutations, as well as new techniques for targeted gene knockouts by homologous recombination and RNA intereference, should make the inactivation of each of these 13,600 genes possible in the near future

The development of the anterior-posterior (AP) axis in the fruit fly depends on the coordinated action of the segmentation genes, which divide the body intothree head, three thoracic, and eight abdominalsegments; and the homeotic genes, which assign aunique identity to each segment.

Embryonic development in Drosophila:

• Development begins with fertilization.

• Prior to fertilization, molecular gradients exist within the eggs. Polar cytoplasm occurs at the posterior end---example of maternal effect.

• 2 nuclei fuse after fertilization to form a zygote.

• 9 mitotic divisions occur without cell division, and after 7 divisions, some nuclei migrate to the polar cytoplasm (posterior) creating germ-line precursors.

• Other nuclei migrate to the cell surface and form blastoderm precursor.

• 4 more mitotic divisions occur and all nuclei are separated by cell membranes.

Subsequent development depends on two processes:

Fig. 19.20,

Adult segmentation reflectEmbryo segmentation

1. Anterior-posterior and dorsal-ventral molecular gradients exist in the egg---mRNAs and proteins placed in egg by mother confer maternal effect.

1. Formation of (1) parasegments and (2)embryonic segments, which give rise to (3) adult segments.

Three major classes of genes control development and differentation

*Mutations identified by presence lethal or abnormal structures during development.

1. Maternal effect genes

1. Segmentation genes

1. Homeotic genes

The four classes of segmentation genes are expressedin the order maternal, gap, pair-rule, and segment polarity.

The maternal genes produce gradients of morphogens.

The gap genes, the first zygotic segmentation genes, are expressed in broad zones along the anterior-posterior axis.

The pair-rule genes subdivide those broad areas into units that span two of the ultimate body segments. The segment polarity genes subdivide the two-segment units into individual segments. In the hierarchy of segmentation gene expression, each gene class is controlled by classes of genes higher in the hierarchy or by members of the same class.

1. Maternal effect genes

Expressed by the mother during egg production; they control polarity of the egg and the thus embryo.

bicoid gene

• Regulates formation of anterior structures (mutants possess posterior structures at each end).

• Gene is transcribed during egg production, and expressed after fertilization.

nanos gene

• Regulates abdomen formation (mRNAs collect in posterior of the egg).

torso gene

• Transcription and translation occur during egg production.

• Occurs throughout the eggs, but is only active at the poles.

Fig. 19.24Distribution of bicoid mRNA and protein in the egg

A = Anterior

P = Posterior

2. Segmentation genes:

Determine the segments of the embryo and adult, and thus divide the embryo into regions that correspond to the adult segmentation patterns.

1. Gap genes Subdivide the embryo along the anterior-posterior axis.

Mutation results in the deletion of several adjacent segments.

1. Pair rule genes Divide the the embryo into regions, each containing

parasegments.

Mutations cause deletions of the same part of a pattern in every other segment.

1. Segment polarity genes Determine regions that become segments of larvae and

adults

Mutants possess parts of segments replaced by mirror images of adjacent half segments.

Fig. 19.25, Functions for segmentation genes defined by mutations.

The homeotic genes are master regulators of othergenes that control the development of segment-specificstructures.

The homeobox in each homeotic gene encodes a homeodomain that allows the gene productsto bind to specific target genes and control their expression.

The homeotic genes are, in turn, regulated by the earlier acting gap, pair-rule, and segment polarity genes.

Homeotic mutations cause particular segments, or parts of them, to develop as if they were located elsewhere in the body. Most homeotic mutations map to the bithorax and the Antennapedia complexes.

3. Homeotic genes:

• Homeotic genes specify the body part to develop at each segment.

• Adult body parts develop from undifferentiated larval tissues called imaginal discs.

• Homeotic mutants develop a different body part at a particular segment (imaginal disc) than the usual body part.

• Different homeotic gene groups share similar sequences of ~180 bp called homeoboxes that code proteins.

• Homeoboxes regulate development and produce proteins that bind upstream of the gene units.

• Homeotic gene complexes are abbreviated Hox.

• Hox genes also specify body plans in vertebrates and plants.

Fig. 19.26

Examples of homeotic Drosophila mutant with the bithorax mutation

What is wrong with one of these flies?

The finding of homeobox genes in other organismssuch as the mouse has made it possible to identify developmentally important genes shared by all animals, demonstrating the evolutionary conservation of gene function.

Fig. 19.28, Organization of bithorax homeotic genes in a 300kb region of the Drosophila genome.

T = thoracic A = abdominal