Survey
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Download powerpoint
Document related concepts
Transcript
Figure 21.1 Chapter 21 Genomes and their Evolution Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Overview: Reading the Leaves from the Tree of Life • Genome sequences exist human, chimpanzee, E. coli, brewer’s yeast, corn, fruit fly, house mouse, rhesus macaque, ………. • Provides information about the evolutionary history of genes and taxonomic groups © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ©Copyright 2011 Pearson Education, Inc. • Genomics is the study of whole sets of genes and their interactions • Bioinformatics is the application of computational methods to the storage and analysis of biological data © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ©Copyright 2011 Pearson Education, Inc. Genome Sequencing • Human Genome Project began in 1990 largely completed by 2003 • 3 stages – Genetic (or linkage) mapping – Physical mapping – DNA sequencing © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ©Copyright 2011 Pearson Education, Inc. • Linkage Mapping maps location of several thousand genetic markers on each chromosome • genetic marker gene or other identifiable DNA sequence • Recombination frequencies used to determine the order & relative distances between genetic markers © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ©Copyright 2011 Pearson Education, Inc. Figure 21.2-1 Chromosome bands Cytogenetic map Genes located by FISH Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 21.2-2 Chromosome bands Cytogenetic map Genes located by FISH 1 Linkage mapping Genetic markers Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 21.2-3 Chromosome bands Cytogenetic map Genes located by FISH 1 Linkage mapping Genetic markers 2 Physical mapping Overlapping fragments Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 21.2-4 Chromosome bands Cytogenetic map Genes located by FISH 1 Linkage mapping Genetic markers 2 Physical mapping Overlapping fragments 3 DNA sequencing Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings • Physical Map distance between genetic markers, (number of bp) • Constructed by cutting DNA molecule into short fragments and arranging them in order by identifying overlaps © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ©Copyright 2011 Pearson Education, Inc. • Sequencing determines the complete nucleotide sequence of each chromosome • Human genome = 3.2 billion bp © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ©Copyright 2011 Pearson Education, Inc. Whole-Genome Shotgun Approach to Genome Sequencing • Developed by J. Craig Venter (1992) • Skips genetic and physical mapping and sequences random DNA fragments directly • Powerful computer programs are used to order fragments © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ©Copyright 2011 Pearson Education, Inc. Figure 21.3-1 1 Cut the DNA into overlapping fragments short enough for sequencing. 2 Clone the fragments in plasmid or phage vectors. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 21.3-2 1 Cut the DNA into overlapping fragments short enough for sequencing. 2 Clone the fragments in plasmid or phage vectors. 3 Sequence each fragment. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 21.3-3 1 Cut the DNA into overlapping fragments short enough for sequencing. 2 Clone the fragments in plasmid or phage vectors. 3 Sequence each fragment. 4 Order the sequences into one overall sequence with computer software. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings • 3-stage process and shotgun used for the Human Genome Project and for genome sequencing of other organisms • Newer sequencing techniques massive increases in speed and decreases in cost $3,000,000,000.00 $1,000.00 © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ©Copyright 2011 Pearson Education, Inc. • Metagenomics environmental sample is sequenced • Eliminates need to culture species in the lab © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ©Copyright 2011 Pearson Education, Inc. Using bioinformatics to analyze genomes and their functions • The Human Genome Project has accelerated progress in DNA sequence analysis © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ©Copyright 2011 Pearson Education, Inc. Centralized Resources for Analyzing Genome Sequences – National Library of Medicine and the National Institutes of Health (NIH) created the National Center for Biotechnology Information (NCBI) – BGI in Shenzhen, China – European Molecular Biology Laboratory – DNA Data Bank of Japan © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ©Copyright 2011 Pearson Education, Inc. • Genbank, the NCBI database of sequences, doubles its data approximately every 18 months • Software is available that allows online visitors to search Genbank for matches to – A specific DNA sequence – A predicted protein sequence – Common stretches of amino acids in a protein • The NCBI website also provides 3-D views of all protein structures that have been determined © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ©Copyright 2011 Pearson Education, Inc. Figure 21.4 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings • Identification of protein coding genes within DNA sequences in a database is called gene annotation • Comparison of unknown genes to known genes in other species provides clues about function © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ©Copyright 2011 Pearson Education, Inc. • Proteomics systematic study of all proteins encoded by a genome © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ©Copyright 2011 Pearson Education, Inc. Figure 21.5 Systems biology approach define gene circuits and protein interaction networks Translation and ribosomal functions Glutamate biosynthesis Mitochondrial functions Vesicle fusion RNA processing Peroxisomal functions Transcription and chromatinrelated functions Metabolism and amino acid biosynthesis Nuclearcytoplasmic transport Secretion and vesicle transport Nuclear migration and protein degradation Mitosis DNA replication and repair Cell polarity and morphogenesis Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Protein folding, glycosylation, and cell wall biosynthesis Serinerelated biosynthesis Amino acid permease pathway Figure 21.5a Mitochondrial functions Translation and ribosomal functions RNA processing Peroxisomal functions Transcription and chromatinrelated functions Metabolism and amino acid biosynthesis Nuclearcytoplasmic transport Secretion and vesicle transport Nuclear migration and protein degradation Mitosis DNA replication and repair Cell polarity and morphogenesis Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Protein folding, glycosylation, and cell wall biosynthesis Figure 21.5b Glutamate biosynthesis Vesicle fusion Serinerelated biosynthesis Amino acid permease pathway Metabolism and amino acid biosynthesis Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Systems Biology in Medicine – The Cancer Genome Atlas project is currently seeking all the common mutations in three types of cancer by comparing gene sequences and expression in cancer versus normal cells – Silicon and glass “chips” have been produced that hold a microarray of most known human genes © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ©Copyright 2011 Pearson Education, Inc. Figure 21.6 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Genomes • By early 2010, 1,200 genomes were completely sequenced, including 1,000 bacteria, 80 archaea, and 124 eukaryotes • Sequencing of over 5,500 genomes and over 200 metagenomes is currently in progress © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ©Copyright 2011 Pearson Education, Inc. Genome Size • Bacteria and archaea 1 to 6 million base pairs (Mb) • Plant & animal greater than 100 Mb; humans 3,000 Mb • Within each domain there is no systematic relationship between genome size and phenotype © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ©Copyright 2011 Pearson Education, Inc. Table 21.1 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Number of Genes • Bacteria and archaea have 1,500 to 7,500 genes • Eukaryotes from 40,000 genes © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ©Copyright 2011 Pearson Education, Inc. • Number of genes is not correlated to genome size • Vertebrate genomes can produce more than one polypeptide per gene because of alternative splicing of RNA transcripts © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ©Copyright 2011 Pearson Education, Inc. Multicellular eukaryotes have much noncoding DNA and many multigene families • Previously called “junk DNA” plays important roles in the cell © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ©Copyright 2011 Pearson Education, Inc. • Sequencing of the human genome reveals that 98.5% does not code for proteins, rRNAs, or tRNAs © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ©Copyright 2011 Pearson Education, Inc. • About 25% of the human genome introns and gene-related regulatory sequences (5%) • Intergenic DNA is noncoding DNA found between genes – Pseudogenes are former genes that have accumulated mutations and are nonfunctional – Repetitive DNA is present in multiple copies in the genome © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ©Copyright 2011 Pearson Education, Inc. • About three-fourths of repetitive DNA is made up of transposable elements © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ©Copyright 2011 Pearson Education, Inc. Figure 21.7 Exons (1.5%) Regulatory sequences (20%) Repetitive DNA that includes transposable elements and related sequences (44%) L1 sequences (17%) Introns (5%) Unique noncoding DNA (15%) Repetitive DNA unrelated to transposable elements (14%) Alu elements (10%) Simple sequence DNA (3%) Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Large-segment duplications (56%) Transposable Elements • First evidence came from geneticist Barbara McClintock’s breeding experiments with Indian corn • Identified changes in the color of kernels that made sense only by mobile genetic elements • Present in both prokaryotes and eukaryotes © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ©Copyright 2011 Pearson Education, Inc. Figure 21.8 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 21.9 Transposon DNA of genome Transposon is copied Mobile transposon Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings New copy of transposon Insertion Figure 21.10 Retrotransposon New copy of retrotransposon Formation of a single-stranded RNA intermediate RNA Insertion Reverse transcriptase Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Sequences Related to Transposable Elements • In primates, a large portion are a family called Alu elements • Function, if any, is unknown © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ©Copyright 2011 Pearson Education, Inc. Other Repetitive DNA, Including Simple Sequence DNA • Many copies of tandemly repeated short sequences • Series of repeating units of 2 to 5 nucleotides is called a short tandem repeat (STR) © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ©Copyright 2011 Pearson Education, Inc. Genes and Multigene Families • Collections of identical or very similar genes © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ©Copyright 2011 Pearson Education, Inc. Figure 21.11 DNA RNA transcripts Nontranscribed Transcription unit spacer -Globin -Globin Heme DNA 18S 5.8S 28S rRNA 28S 5.8S 18S (a) Part of the ribosomal RNA gene family Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings -Globin gene family Chromosome 16 Embryo 2 1 2 1 -Globin gene family Chromosome 11 G A Fetus and adult Embryo Fetus Adult (b) The human -globin and -globin gene families Duplication, rearrangement, and mutation of DNA contribute to genome evolution • Earliest forms of life minimal number of genes, (only those necessary for survival and reproduction) • Size of genomes has increased over evolutionary time, (extra genetic material raw material for gene diversification) © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ©Copyright 2011 Pearson Education, Inc. Alterations of Chromosome Structure • Humans have 23 pairs of chromosomes, while chimpanzees have 24 pairs • 2 ancestral chromosomes fused in the human line © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ©Copyright 2011 Pearson Education, Inc. Figure 21.12 Human chromosome 2 Chimpanzee chromosomes Telomere sequences Centromere sequences Telomere-like sequences 12 Human chromosome 16 Centromere-like sequences 13 (a) Human and chimpanzee chromosomes Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Mouse chromosomes 7 8 (b) Human and mouse chromosomes 16 17 Evolution of Genes with Related Functions: The Human Globin Genes • Globin genes evolved from common ancestral globin gene, which duplicated and diverged about 450–500 mya • Differences arose from accumulation of mutations © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ©Copyright 2011 Pearson Education, Inc. Figure 21.14 Ancestral globin gene Evolutionary time Duplication of ancestral gene Mutation in both copies Transposition to different chromosomes Further duplications and mutations 2 1 2 1 -Globin gene family on chromosome 16 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings G A -Globin gene family on chromosome 11 Evolution of Genes with Novel Functions • Some duplicated genes have diverged so much that the functions of encoded proteins are now very different • e.g. lysozyme gene was duplicated and evolved into the gene that encodes α-lactalbumin in mammals (milk production role) © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ©Copyright 2011 Pearson Education, Inc. Rearrangements of Parts of Genes: Exon Duplication and Exon Shuffling • Has contributed to genome evolution • Mixing and matching of exons © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ©Copyright 2011 Pearson Education, Inc. Figure 21.15 EGF EGF EGF EGF Epidermal growth factor gene with multiple EGF exons F F F Exon shuffling Exon duplication F Fibronectin gene with multiple “finger” exons F EGF K K K Plasminogen gene with a “kringle” exon Portions of ancestral genes Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Exon shuffling TPA gene as it exists today How Transposable Elements Contribute to Genome Evolution • Multiple copies of similar transposable elements may facilitate recombination, or crossing over, between different chromosomes • Insertion of transposable elements within a protein-coding sequence may block protein production • Insertion of transposable elements within a regulatory sequence may increase or decrease protein production © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ©Copyright 2011 Pearson Education, Inc. • Transposable elements may carry a gene or groups of genes to a new position • Transposable elements may also create new sites for alternative splicing in an RNA transcript • In all cases, changes are usually detrimental but may on occasion prove advantageous © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ©Copyright 2011 Pearson Education, Inc. Comparing genome sequences provides clues to evolution and development • Genome comparisons of closely related species help us understand recent evolutionary events • Genome comparisons of distantly related species help us understand ancient evolutionary events • Relationships among species can be represented by a tree-shaped diagram © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ©Copyright 2011 Pearson Education, Inc. Figure 21.16 Bacteria Most recent common ancestor of all living things Eukarya Archaea 4 1 3 2 Billions of years ago 0 Chimpanzee Human Mouse 70 60 50 40 30 20 Millions of years ago Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 10 0 Comparing Distantly Related Species • Highly conserved genes have changed very little over time • Clarify relationships among species • Bacteria, archaea, and eukaryotes diverged from each other between 2 and 4 billion years ago • Results from model organisms applied to other organisms © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ©Copyright 2011 Pearson Education, Inc. Comparing Closely Related Species • Human and chimpanzee genomes differ by 1.2%, at single base-pairs, and by 2.7% because of insertions and deletions • Several genes are evolving faster in humans than chimpanzees • These include genes involved in defense against malaria and tuberculosis, regulation of brain size, and genes that code for transcription factors © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ©Copyright 2011 Pearson Education, Inc. • Humans and chimpanzees differ in the expression of the FOXP2 gene, (vocalization gene) • May explain why humans but not chimpanzees communicate by speech © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ©Copyright 2011 Pearson Education, Inc. Comparing Genomes Within a Species • Human species only 200,000 years old low within-species genetic variation • Variation due to single nucleotide polymorphisms, inversions, deletions, and duplications • Variations useful for studying human evolution and human health © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ©Copyright 2011 Pearson Education, Inc. Comparing Developmental Processes • Evolutionary developmental biology, or evo-devo, is the study of the evolution of developmental processes in multicellular organisms • Minor differences in gene sequence or regulation can result in striking differences in form © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ©Copyright 2011 Pearson Education, Inc. Widespread Conservation of Developmental Genes Among Animals • Molecular analysis of the homeotic genes in Drosophila has shown that they all include a sequence called a homeobox • An identical or very similar nucleotide sequence has been discovered in the homeotic genes of both vertebrates and invertebrates • Homeobox genes code for a domain that allows a protein to bind to DNA and to function as a transcription regulator • Homeotic genes in animals are called Hox genes © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ©Copyright 2011 Pearson Education, Inc. Figure 21.18 Adult fruit fly Fruit fly embryo (10 hours) Fly chromosome Mouse chromosomes Mouse embryo (12 days) Adult mouse Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 21.18a Adult fruit fly Fruit fly embryo (10 hours) Fly chromosome Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 21.18b Mouse chromosomes Mouse embryo (12 days) Adult mouse Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings • Related homeobox sequences have been found in regulatory genes of yeasts, plants, and even prokaryotes • In addition to homeotic genes, many other developmental genes are highly conserved from species to species © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ©Copyright 2011 Pearson Education, Inc. • Sometimes small changes in regulatory sequences of certain genes lead to major changes in body form • For example, variation in Hox gene expression controls variation in leg-bearing segments of crustaceans and insects • In other cases, genes with conserved sequences play different roles in different species © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ©Copyright 2011 Pearson Education, Inc. Figure 21.19 Thorax Genital segments Thorax Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Abdomen Abdomen Comparison of Animal and Plant Development • In both plants and animals, development relies on a cascade of transcriptional regulators turning genes on or off in a finely tuned series • Molecular evidence supports the separate evolution of developmental programs in plants and animals • Mads-box genes in plants are the regulatory equivalent of Hox genes in animals © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ©Copyright 2011 Pearson Education, Inc. Figure 21.UN01 Bacteria Genome size Number of genes Gene density Introns Other noncoding DNA Archaea Most are 16 Mb 1,5007,500 Higher than in eukaryotes None in protein-coding genes Present in some genes Very little Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Eukarya Most are 104,000 Mb, but a few are much larger 5,00040,000 Lower than in prokaryotes (Within eukaryotes, lower density is correlated with larger genomes.) Unicellular eukaryotes: present, but prevalent only in some species Multicellular eukaryotes: present in most genes Can be large amounts; generally more repetitive noncoding DNA in multicellular eukaryotes Figure 21.UN02 Human genome Protein-coding, rRNA, and tRNA genes (1.5%) Introns and regulatory sequences (26%) Repetitive DNA (green and teal) Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 21.UN03 -Globin gene family -Globin gene family Chromosome 16 2 1 2 1 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Chromosome 11 G A Figure 21.UN04 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 21.UN05 Crossover point Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 21.UN06 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
