Lectures 1 and 2-Origins of Genes/Genomes

what is a gene?

a defined stretch of DNA encoding a specific protein or ribonucleic acid

or can be considered as an open reading frame (ORF), as identified in genome sequences often by computers

ENCODE project gene definition

a locatable region of genomic sequence, corresponding to a unit of inheritance, which is associated with regulatory regions, transcribed regions, and/or other functional sequence regions

what is a genome?

the entire genetic component of a living organism

does a species have a genome?

different strains of E coli often share <40% of their genes

prokaryotic genomes are evolutionary mosaics

concept of prokaryotic species is problematic

is there a human genome?

yes and no

publicly sequenced genome is a composite of data from 4 DNA samples chosen at random from dozens of samples provided by anonymous volunteers

genes vary between individuals and within individuals

is the genome of an individual stable?

no, copy number variation (CNV) between and within individuals (i.e. in the brain)

cancer

genomics

sequencing genomes of cultured microorganisms, animal/plant tissue samples, etc.

re-sequencing

a part of genomics, determining the sequence of a genome for the purposes of comparison to a reference genome (e.g. multiple human genomes, strains of E coli, etc)

transcriptomics

traditional approach: sequencing of ESTs (expressed sequence tags—cDNA derived from mRNAs)

evolved into RNA-seq technology

RNA-seq technology

whole transcriptosome shotgun sequencing, which uses next-gen technologies to provide a comprehensive picture of the RNA present in a sample

has begun to replace microarray technologies as a tool of choice for gene expression studies

metagenomics

culture-independent sequencing

DNA isolated from a community of organisms, shotgun sequenced, and assembled

goal is to gain insight into the composition of the microbial community

community can be anything: soil, water, air, gut contents, feces, etc

proteomics

generally refers to large-scale experimental analysis of proteins in complex mixtures, but smaller partially purified samples can also be examined

large-scale studies combine fragmentation of proteins, separation of proteins by liquid chromatography and detection by tandem mass spectrometry

requires a reference genome with predicted proteins, which are digested in silico. peptide fragments from the biological sample are compared to the in silico predictions—if a match, then protein is present

metabolomics

study of small-molecule metabolite profiles using gas chromatography, high performance liquid chromatography, etc for sample separation, and mass spectrometry for detection

can provide insight into the physiology of the cell at the time the sample was taken

where do genes and genomes come from?

from the first living things

through comparing extant (living) and extinct (via fossils and indirect evidence), we infer that shared traits originated in a common ancestor

feasibility experiments

test hypotheses about the origin of life by demonstration of similar events in the lab

e.g. Miller-Urey experiment of 1952: water + methane + ammonia + hydrogen + electricity = amino acids

relics

examine fossils (biological or chemical) or putatively primitive features of modern organisms

e.g. organisms that were around ~3 billion years ago

• fossilized stromatolites suggest cyanobacteria were around ~2.7 BYA

• 2-methylhopanoids serve as membrane biomarkers for cyanobacterial oxygenic photosynthesis at around that time

comparative biology

compare and contrast properties of living beings, infer what the biology of the last universal common ancestor (LUCA) might have been like

e.g. which came first, RNA or DNA? what was the genetic code like?

ancient DNA research

genomes of extinct organisms (e.g. neanderthals, mammoths, etc) have been sequenced but DNA degrades very quickly (upper limit of DNA preservation is thought to be ~1 million years)

RNA world

era during which the genetic information resided in the sequence of RNA molecules and the phenotype derived from the catalytic properties of RNA

preceded DNA and protein based life

which came first, DNA or protein?

need DNA to store information to make proteins, but need protein to synthesize DNA

likely, neither came first

likely was RNA with catalytic activity

RNA with catalytic activity and origin of life

can replicate itself and synthesize peptides

with mutation, chemical selection leads to proteins, enzymes, complex systems, which eventually leads to cells and natural selection

compartmentalization and the RNA world

important, served to bring metabolites in close proximity

hard to reason how complex metabolism evolved otherwise

RNA world stages

pre-biotic chemistry → nucleic acid precursors → polymerization catalyzed by minerals → random sequence RNAs, some with very modest self-replication ability → better and better mutant replicators selected (darwinian evolution begins here) → RNAs with metabolic activity, specialized replicators → self-assembled membrane, metabolism, RNA organism

examples of RNA-mediated biochemistry found

all across the tree of life (e.g. importance of non-coding RNAs in gene expression, genome defense, etc)

RNA may have been preceded by

some other replicating, catalytic molecule, in the same way that DNA and proteins seem to have been preceded by RNA

while the modern cellular world is one of ribonucleoproteins,

most enzymes are proteins (20 amino acid character states, much greater potential for structural/functional diversity)

last universal common ancestor (LUCA)

can make inferences on this based on protein/DNA sequence similarity, such as that it had a double stranded DNA genome, genes involved in housekeeping function and core metabolic functions

housekeeping functions for genes

transcription, translation, DNA replication, protein folding and turnover, etc

core metabolic functions of genes

amino acid metabolism purine/pyrimidine biosynthesis, carbon metabolism

where do new genes come from?

from pre-existing genes (either from within the genome, or duplication, or acquired from another organism by horizontal gene transfer, HGT)

from non-coding DNA (‘from scratch’)

gene duplication examples

globin gene family- have myoglobin branch, alpha family branch, beta family branch, this all influences arrangement in humans

• over evolutionary time, duplication, mutation, transposition, duplications and mutations occurred to get us to these families

tubulin gene family

HSP90 gene family- eukaryotes have cytosolic and ER isoforms that evolved by duplication

% of duplicate genes in homo sapiens

38%

homologs

in evolutionary biology, genes/proteins that share common ancestry

orthologs

genes/proteins in different species that evolved from a common ancestral gene by speciation

• genes diverging due to species lineages separating

these genes/proteins typically have the same function in different species

paralogs

genes within a genome that are related to one another by gene duplication, often evolve new functions

• genes evolving in parallel with species after a duplication

DNA-based duplication

usually involved transposable element or other type of repeated element

may occur by unequal crossing-over mediated by these elements

different fates for resulting genes

• may acquire new functions by evolving new expression patterns or novel biochemical protein/RNA functions

RNA-based duplication

termed retroposition or retroduplication

new retroposed gene copies may arise through reverse transcription of mRNA from parental source genes

functional retrogenes with new functional properties may evolve from these copies after acquisition or evolution of promoters in their 5’ flanking regions that may drive transcription

DNA-based gene fusion

origin of new chimeric gene or transcript structures

partial duplication (hence fission) of ancestral source genes precedes juxtaposition of partial duplicates and subsequent fusion (presumably mediated by evolution of novel splicing signals and/or transcription termination/polyadenylation sites)

transcription-mediated gene fusion

novel transcript structures may arise from intergenic splicing after evolution of novel splicing signals and transcriptional readthrough from upstream gene

new chimeric mRNAs may sometimes be reserve transcribed to yield new chimeric retrogenes

what causes new chimeric transcripts?

exons, transcriptional start sites, constitutive splicing, splicing of ancestral gene structures, intergenic splicing

orphan genes

genes without obvious homologs in the genomes of other organisms (OFRans)

can evolve by gene duplication coupled with extreme sequence divergence (evolve to the point that homology cannot be detected using sequence and structure based comparisons), or non-coding DNA

how to find a new gene (comparative genomics)

one should show that corresponding DNA region is present in related species and synthetic in these species

region should still be alignable- the species compared should be sufficiently close to each other to ensure that even neutrally diverging sequences have not yet acquired too many mutation

finally, all outgroups should not have a sign of a gene in respective position, possibly apart of the most closely related ones, which could have a protogene or an RNA gene in the position

life cycles of genes

1. gene → pseudo-gene (loss of translation, transcription → gene death) → non-genic sequence

2. gene → proto-gene (gain of transcription, translation → gene birth) → non-genic sequence

3. gene → single copy → multiple copies (via duplication) → function x, y

gene duplication is a significant force in

evolution of cells and their genomes

for any given gene family/genome, birth rate and fate of duplicate genes is influenced by:

• intrinsic rate of duplication (how much repetitive DNA? abundance of mobile elements? can vary greatly)

• intrinsic features of DNA recombination machinery (some more recombinagenic than others)

• structure of gene families (present in arrays like rRNA or dispersed in genome? impacts frequency of gene conversion/unequal crossing over)

• population size of organism (impacts likelihood that duplicate gene will become fixed)

• impact of newly evolved duplicate genes on organism (positive, negative, neutral)