Multigene families with identical genes

In some cases, in order to produce large quantities of a gene product, many copies of identical genes are required. These, genes may occur in the form of repeat units, each comprising of (i) a coding region, which is highly conserved to produce exactly the same gene product, and (ii) a spacer region, which may show divergence. Some examples of these multigene families will be described in this section.

Multiple copies of histone genes. The five major histone proteins, namely H_1; H₂A, H₂B, H₃, H₄ are involved in the packing of DNA into nucleosomes, the chromatin subunits. When DNA is duplicated during S phase of the cell cycle, large quantities of these histone proteins are needed. To meet this demand, for each of the histone genes, there are present (i) 10-20 copies in birds and mammals and (ii) 600-800 copies in sea urchin and newt (amphibians). A higher number in amphibians suggests a response to their need for rapid cell division. The five genes for five histones form a basic unit that is repeated, although different genes within a repeat unit may differ in orientation (Fig. 44.5). These genes (coding sequences) in a repeat unit are highly conserved, but the spacer region differs in different organisms. The histone genes differ from most other eukaryotic genes in haying their transcripts devoid of introns and poly A tails.

Another interesting feature of the multigene family of histone genes observed in Drosophila is the presence of an 'attachment site' per repeat unit (Fig. 44.6), 100 such repeat units being present in each haploid genome. With the help of attachment site, the genes remain attached to nuclear scaffold (scaffold is the protein backbone of chromosomes, to which DNA remains attached). These attachment sites help in transcription.

Ribosomal RNA (rRNA) genes in tandem arrays. For the production of about 10 million ribosomes per cell in eukaryotes, rRNA genes are present in multiple copies at nucleolar organizing regions (NOR) of specific satellited chromosomes.

The number of these genes may vary from 50-30,000 in a cell and this number may be unequally distributed on NORs, if more than one such loci are present. The DNA comprising these genes is called rDNA (ribosomal DNA), which is repetitive in nature. Each repeat unit has (i) a coding region with genes that specify 18S, 5.8S and 28S rRNA molecules, (ii) a spacer region called intergenic spacer (IGS) and (iii) internal transcribed spacers (ITS) one each between 18S and 5.8S genes and between 5.8S and 28S genes. Since parts of IGS region adjoining the coding region, known as external transcribed spacers (ETS), is also transcribed, the use of the term non-transcribed spacer (NTS) for the whole spacer region has been considered to be inappropriate. Actually, the NTS makes only a part of the IGS (Fig. 44.7), the remaining part of IGS being ETS. The IGS in its turn has a region consisting of a tandem array of variable number of subrepeats ranging from 100-300 bp (bp = base pairs) in length. The variation in number and size of the subrepeats in IGS is responsible for variation in length of the repeat unit (IGS + coding region).

The rDNA repeat units are usually looped off from the main chromosome fibre, in the form of extended threads at nucleolar organizing region. These loops, in association with specific proteins form the nucleoli, where rRNA synthesis and processing really takes place. The number of nucleoli and, therefore, that of the nucleolar organizing (satellited) chromosomes in an organism may vary from one to several. At each locus (NOR), rDNA repeat units may evolve independently both in length and also in the nucleotide sequence of the spacer region, so that the length of the repeat unit including coding and spacer regions (non-transcribed spacer or NTS; external transcribed spacer or ETS and internal transcribed spacers or ITS) varies from about 7 kb (kilobase pairs) to 14 kb. In wheat and barley, it is usually 9 kb-10 kb (Fig. 44.8).

5S RNA genes. 5S RNA genes are present independently of the rDNA which is localized at the NOR in eukaryotes (5S RNA is also found in ribosomes). However, in prokaryotes and yeast, 5S RNA genes are present in close vicinity of rDNA (Fig. 44.9). The 5S RNA genes are also organized in tandem repeats, each repeat consisting of a gene 120 bp long and a spacer region. The length of the complete repeat is 375 bp in Drosophila. In wheat, there are two loci for 5S RNA having repeats of different lengths, 480 bp and 500 bp. These repeat units may sometimes carry pseudogenes instead of genes, and may not synthesize any RNA.

tRNA multigene families. The genes for each of the different tRNAs are also found in multiple copies to meet the heavy demands of the cell for the production of tRNA molecules. Ten to several hundred genes for each tRNA are present in each haploid genome. While in some cases with fewer copies of a gene, these copies are dispersed, in other cases like Xenopus (a toad), tandem repeats of long sequences (each repeat having genes for several different tRNAs) are found. For instance, in Xenopus, a 3.2 kb repeat length has 8 genes, 2 for tRNA_f^met and six others for six different tRNA molecules (Fig. 44.10). In still other cases (e.g. Drosophila), genes for completely different tRNA species are clustered over a length of several thousand base pairs. Sometimes, tRNA pseudogenes are also found.

Small nuclear RNA (SnRNA) genes. Small nuclear RNAs (SnRNAs) are found in abundance in the nuclei of all eukaryotes and represent neither tRNA, nor rRNA. Six SnRNAs, that are usually found, range from 100(U6) to 215(U3)nucleotides in length and are involved in RNA processing through formation of SnRNP (small nuclear ribonucleoproteins; see Expression of Gene : Protein Synthesis 2.  Transcription in Prokaryotes and Eukaryotes). These are encoded by multiple copies of identical genes organized in tandem arrays of repeat units, each SnRNA gene being flanked on either side by spacer DNA ranging from 800 bp to 45,000 bp in length in different organisms.

An unexpected feature of the DNA that is complementary to SnRNAs is that it consists of many more pseudogenes than the functional genes (10 : 1). For instance in humans there are 30 genes, for Ul (an SnRNA) on chromosome 1 and 500-1000 pseudogenes distributed throughout the genome.

Multigene families for storage proteins in crop plants. In recent years, extensive studies on the genetics of storage proteins in several crop plants have also been undertaken. It has been shown that these storage proteins are encoded by multigene families, and are represented mainly as prolamins (major storage proteins in cereals - soluble in aqueous alcohol) or globulins (major storage proteins in legumes - soluble in salt). Three to ten genes for each of the ten prolamin families are reported in maize; more than a dozen genes for prolamins represent several families in wheat; and 18 genes belonging to three families of globulin genes are known in pea. Homologies in genes coding for prolamins and globulins in different crop plants has also been shown. Their multiplicity conveniently meets the demand for rapid synthesis for these proteins in the developing seeds.