Chromosome Structure Introductory article N Patrick Higgins, University of Alabama, Birmingham, Alabama, USA Article Contents . Abundance Genes are organized into discrete cellular structures called chromosomes that coordinate . Chromosome Size DNA replication and distribution of replicated genetic copies between two daughter cells. Plasmids As vehicles of genetic transmission, chromosomes play a central role in Darwinian . Chromosome Shape evolution. Enzymes of DNA Topology . Chromatin Abundance . DNA Replication . Eukaryotic Segregation Biology is divided into three great kingdoms: Eubacteria, . Transcription Archaea and Eukaryota. Bacteria (Eubacteria and Ar- . Recombination chaea) are ubiquitous in the environment, and these small . Chi Sites single-celled organisms grow over an amazingly wide range . Transposons ofenvironmental conditions. For example, bacteria can . Site-specific Recombination grow at temperatures below freezing, and certain members ofthe archaea can grow at depths ofover three miles and at temperatures exceeding 6008F and 200 atmospheres of pressure. Eukaryotes, which include the more conspicuous genome yet analysed is that of Myxococcus xanthus, with fungi and all plants and animals, are usually recognized as 9.2 Mbp (9 200 000 bp). However, the best studied organ- the predominant life forms on earth. They are subjects of ism in nature is E. coli, which has a 4.6-Mbp chromosome great biological interest and they differ from bacteria by with 4288 genes for proteins, seven operons for ribosomal having a larger cell size and by compartmentalizing ribonucleic acids (RNAs), and 86 genes for transfer RNAs. chromosomal deoxyribonucleic acid (DNA) in a nucleus, The E. coli chromosome contains numerous gene which separates it from the protein-making cytoplasm. families, each family having evolved from a common None the less, considering the large cell numbers and wide ancestor. The largest gene family is comprised of 96 three- environmental growth ranges, bacteria easily account for component (ABC) transporters, which are membrane- the majority ofDNA biomass on earth. bound machines that import and export a variety ofsmall The chromosome is the heart ofa central paradox in molecules and proteins. By contrast, the smallest free- evolution. How do species in the three kingdoms remain living organism is Mycoplasma genatalium with a 0.58- the same over long periods ofgeological time and also Mbp genome that encodes 468 protein genes, one generate sufficient variability to produce new species, ribosomal RNA operon and one ABC transporter. Both sometimes relatively rapidly? Stability versus change is a E. coli and M. genatalium have complete information for crucial dichotomy in molecular biology. The events that the synthesis ofcell walls, cell membranes and critical bring about stability and change in DNA structure involve enzymes ofintermediary metabolism, plus the RNA processes ofreplication, transcription and recombination. molecules, ribosomal proteins and a clutch ofenzymes Similar mechanisms operate in the three living kingdoms, (the replisome) to replicate DNA efficiently. Putative but the key molecular mechanisms that control and functions for about a quarter of the genes of E. coli remain catalyse these events are understood best in a eubacterium: to be discovered. A reasonable estimate is that 150–200 Escherichia coli. protein-encoding genes would be ‘essential’ for a basic bacterial lifestyle (in a rich medium). Eukaryotic organisms generally have larger chromo- somes than bacteria. For example, the yeast Saccharo- myces cerevisiae has about 6000 genes (50% more than E. Chromosome Size coli), whereas mammalian cells contain 1000 times (per haploid equivalent) the DNA ofan E. coli cell. In humans Free-living bacteria need genetic information to synthesize the 5000 Mbp ofhaploid DNA is distributed among 22 proteins for executing vital functions. Most bacteria have a autosomes and two sex-specific chromosomes. Eukaryotic single chromosome with DNA that is about 2 Mbp (mega DNA is localized in a compartment, the nucleus, which is base pairs) long (1 Mbp 5 1 000 000 base pairs), but the separated by a phospholipid-containing membrane from DNA content ofdifferent species varies from0.58 to cytoplasmic ribosomes and protein translation activity. greater than 9 Mbp ofDNA, and some bacteria have During cell division, the eukaryotic nuclear membrane multiple chromosomes. For example, Leptospira has two chromosomes of4.4 and 4.6 Mbp and the largest bacterial ENCYCLOPEDIA OF LIFE SCIENCES / & 2001 Macmillan Publishers Ltd, Nature Publishing Group / www.els.net 1 Chromosome Structure breaks down once per cell cycle to distribute the 46 diploid Plectonemic Paranemic chromosomes equally between two daughter cells. Plasmids 5kbp In addition to the large chromosome, many (most?) Plasmid bacteria have additional DNA molecules called plasmids (or episomes.) Plasmids are separate DNA molecules that contain a replication origin which allows them to multiply independently ofthe host chromosome. Plasmids range in size from 1 kbp (Kilo base pair) (1000 bp) to 100 kbp, and these DNA molecules encode genetic systems for specia- Eukaryotic chromatin Prokaryotic chromatin lized functions. Some plasmids make extracellular appen- Gyrase dages that allow bacteria to infect and colonize sensitive Histone eukaryotic hosts. Plasmids often carry genes that confer on Solenoidal assembly bacteria the ability to survive in the presence ofantibiotics supercoils σ such as tetracycline, kanamycin and penicillin. Many = –0.05 HU H-NS plasmids also contain genes that promote DNA transfer so Deproteinate that plasmid genes can move into other bacterial species. Plasmid transfer has caused the emergence of bacterial pathogens that are resistant to most ofthe useful Interwound antibiotics in medicine, with notable examples including supercoils (a) σ = –0.05 multidrug-resistant strains of Staphylococcus and Myco- bacterium tuberculosis. In most eukaryotes, plasmids are rare. However, S. Topo cerevisiae contains a plasmid called the 2-m circle which IV efficiently partitions to new daughter cells at every cell Topo division. This DNA serves as a convenient module for gene II cloning and performing genetic experiments in yeast. (b) Figure 1 (a) DNA is a plectonemic helix (left) rather than a paranemic helix (right), and thus it must spin axially to undergo replication, transcription and extended pairing for homologous recombination. Chromosome Shape Supercoiling in circular bacterial chromosomes is maintained by the concerted action of DNA gyrase, which introduces negative supercoils at On a macroscopic scale, bacterial chromosomes are either the expense of adenosine triphosphate (ATP) binding and hydrolysis, and circular or linear. Circular chromosomes are most TopoI plus TopoII, which remove excess negative supercoils. Negative common, at least among the best-studied bacteria. How- supercoiled DNA adopts an interwound conformation. However, ‘solenoidal’ supercoils can be stabilized when DNA is wrapped on a protein ever, the causative agent ofLyme disease, Borrelia surface. This is the mechanism of supercoil formation in mammalian cells burgdorphei, has a 2-Mb linear chromosome plus 12 (centre left). Most bacteria have nonspecific DNA-binding proteins such as different linear plasmids. Eukaryotic chromosomes are HU and H-NS, which stabilize supercoils but are much less effective at invariably linear, and they have two ends, each carrying a condensing DNA compared with true histones (centre right). (b) Bacteria special structure called a telomere, and a organized region and eukaryotes both have an enzyme, TopoIV and TopoII respectively, designed to unknot and untangle DNA. called the centromere which allows the chromosome to attach to cellular machinery that moves it to the proper place during cell division. DNA synthesis the rotation speed approaches 6000 rpm. One critical facet of chromosome structure is that DNA Chromosomal DNA molecules are very long and thin, so is a plectonemic helix, which means that two helical strands DNA must fold many times to fit within the confines of a entwine about each other. For duplex DNA the two bacterial cell. How does DNA twisting transpire without antiparallel strands, often referred to as the Watson and chromosomes getting tangled up? The problem was Crick (red and blue in Figure 1), are interwound once for important enough that Watson and Crick considered a every 10 bp. Because ofthis wound configuration, bio- paranemic helix, which is a pair ofcoils that lay side by side chemical transactions that involve strand separation without interwinding. Strands ofa paranemic helix can require chromosome movement (spin) about DNA’s long separate without rotation (Figure 1). None the less DNA is axis. The processes ofDNA replication, recombination plectonemic, and keeping chromosomes untangled re- and transcription all require DNA rotation, and during quires a special class ofenzymes called topoisomerases. 2 ENCYCLOPEDIA OF LIFE SCIENCES / & 2001 Macmillan Publishers Ltd, Nature Publishing Group / www.els.net Chromosome Structure Enzymes of DNA Topology enzyme such as gyrase, eukaryotic DNA is wrapped tightly around nucleosomes, generating solenoidal supercoils that The enzymes that solve the untangling problem are condense DNA 8-fold (Figure 1). A nucleosome contains topoisomerases. Topoisomerases break and rejoin DNA four subunits: histones H2A, H2B, H3 and H4. If histones molecules, thereby allowing individual strands to pass