The Origins of Life: From RNA World to LUCA

Posted on May 17, 2024 in Biology

In order for a system to reproduce

Ordered accumulation of biomass

Energy harvesting processes

Network of chemical reactions – metabolism

Memory

Respond to changes in the environment

When did life begin on Earth?

Upper and lower boundaries

The first time point at which life could have existed (lower)

When life was definitely present (upper)

Estimation of Earth’s age

Age of solar system: Astronomical/planetological studies

Geological approach: Radioisotope dating of ancient rocks.

Our solar system was formed by condensation of a rotating mass of gas and dust.

Earth’s atmosphere was first composed of Helium and Hydrogen.

The presence of oxygen is mostly due to ancient photosynthetic organisms.

Gradual Increase in Atmospheric O₂?

The great oxygenation event: Caused by cyanobacteria doing photosynthesis!

Cambrian explosion

Huronian glaciation: Between 2.45 – 2.22 Ga.

When Did Life Begin?

• Most probable estimate: between 3.9-4.2 Bya
• About 0.4 – 0.7 By after Earth formation.
• Compared to the current age of Earth, not much time was wasted.

Evidence for “when” comes from:

• Ancient microfossils
• Stromatolites
• Isotopic abundances in oldest rocks – zircon

Seven Steps

1. The generation of simple organic molecules from inorganic molecules.
2. Chemical “evolution” to produce complex organic complexes.
3. The origin of self-replication and the creation of “genotypes”.
4. Compartmentalization and creation of cells.
5. The linking of “genotype” and “phenotype”.
6. The origin of the genetic code.
7. The takeover of early replication systems by one involving DNA.

Where did molecules come from that were required for life to begin?

• Synthesis of urea from simple organic components was demonstrated as far back as in 1828 (Friedrich Wöhler).
• Alanine was synthesized from formamide, water and UV irradiation (1850s).
• Sugars were made from formaldehyde and NaOH (1850s).
• By the time Origin of Species was published it was already known that organic molecules can be made from inorganic compounds.
• J.B.S. Haldane and A. I. Oparin independently suggested that early Earth conditions helped in making organic molecules that could have been the precursors of life (1920s/30s).

Limitations of M-U experiments

• Not all organic molecules are formed.
• No living organism or self-replicating chemical was formed.

Why?

• Need for more time (millions of years not a few weeks or months).
• Maybe some key ingredient is missing.
• Maybe the basic idea is wrong!

Main problems of prebiotic chemistry in aqueous solution

• Very low concentration of reactants.
• Where do monomers come from (building blocks)?
• Polymerization: Hydrolysis and not polymerization occurs!!

Did Natural Selection Act on These Molecules?

• Selection criteria – stability and speed of assembly.
• The key is the ability for evolution by natural selection to occur.
• Require polymers copying themselves.
• Mechanism of heritability.
• Nucleic acid polymers – potential for self-replication.
• The entire mechanism of self-replication can be called as “replicase”.

Arguments against Arsenic substitution

• All experiments, their design and execution, are flawed.
• Their DNA and protein isolation methods were shabby.
• It is hard to distinguish P from As.
• Arsenate is not a stable compound.
• Arsenate triesters have a half-life of only a few ms & arsenate-DNA of about 1 m.
• Arsenate incorporation into DNA requires 8-10 biochemical steps.
• Bacteria may have to develop a completely different biochemistry.
• Even very pure arsenate has phosphate contamination.

How about a silicon-based life?

• All known life on Earth is built upon carbon and carbon-based compounds.
• Yet the possibility has been discussed that life elsewhere may have a different chemical foundation – one based on the element silicon.
• Silicon is just below C in the periodic table, also a p-block element of group 4.
• Has similar chemistry: Ex: carbon combines with 4 H atoms to form methane, CH₄, silicon yields silane, SiH₄. Silicates are analogs of carbonates.
• Fatal Flaws: Is that SiO₂ the waste produced during respiration is actually a solid! Silicon compounds are not chiral.
• So far no organic compound with silicon has been found.

A silicon-based life-form, the Horta, was discovered by miners on Janus VI in one of the Star Trek episodes. Every 50,000 years, all the Horta die except for one individual who survives to look after the eggs of the next generation.

Why RNA?

The known biological functions of RNA continue to grow.

• RNA has been transformed from a molecule with a minor role in protein synthesis, to an important player in all of molecular biology and evolution.
• Just about 20 years ago, messenger RNA was thought to be a passive carrier of genetic information from DNA and its conformation random or irrelevant.
• Ribosomal RNA was believed to be a scaffold for the essential ribosomal proteins, and the transfer RNAs simply dull adapters that placed each amino acid in the location specified by the genetic code.
• Now we know that the ribosomal proteins mainly provide the scaffold that allows the ribosomal RNAs to catalyze peptide bond formation.

Difference between DNA and RNA

• RNA is capable of having complex structures.
• Secondary and tertiary structures.
• It can also “fold”.

Why are ribozymes critical for an RNA world hypothesis?

Catalysis

Self-replication + nucleotide = RNA-dependent RNA polymerase activity

SELEX (Systematic evolution of ligands by exponential amplification)

Or In vitro selection is the basis for most hypotheses on the RNA world.

• Nucleic acid pool/target/Incubation of pool with target/Removal of non-binding species/Elution of RNA from target/Re-amplification of binding species.

Metabolic function in the RNA world

It is quite possible that the RNA world was complex enough to have some sort of metabolism.

• Some form of metabolic support system might have existed.
• Increase in order by incorporation of NTPs into a polymer by expenditure of the energy.
• Starting materials: ribose, phosphate, purines and pyrimidines.

Limitations of RNA as a catalyst

• Very limited catalytic capability.
• In vitro selection method yielded very few catalytic RNAs. For example, to have a 50% chance of obtaining a single RNA molecule capable of catalyzing a template-directed ligation reaction by a modest (by protein standards) factor of 10,000, Bartel and Szostak in 1993 estimated that one must sift through 2 × 10¹³ random RNA sequences 220 nucleotides in length as against only 10⁷ in the case of peptide (Bartel and Szostak 1993).
• Obtaining RNA catalysts for various reactions have failed.
• Peptide is 10% the size of an RNA catalytic motif.
• Peptides are 10⁶ times “fitter” as catalysts than RNA.

Transition to the DNA–protein world

• RNA – great genetic molecule/can evolve to perform a broad range of catalytic tasks.
• RNA – limited chemical functionality, not equipped to meet the challenges of the environment.
• The invention of protein synthesis, instructed and catalyzed by RNA, was the crowning achievement of the RNA world.

The Biological stage: The “two-biopolymer” system DNA RNA Protein

• It is highly unlikely that the complete system evolved at once…from scratch.
• One of the 3 polymers must have the self-replicated property.
• Francis Crick suggested in 1960 that RNA could serve as both carrier and catalyst for information.
• RNA could have been both phenotype and genotype.
• The role of DNA in today’s world is very “limited”.
• RNA is far more diverse.

Protocell Assembly

• Could form spontaneously as new membranes self-assemble and encapsulate genetic molecules in solution.
• Montmorillonite is not only a catalyst of RNA polymerization but can also catalyze membrane assembly.
• The hollow channels within the rocks, especially, in hydrothermal vents can provide a protected compartmentalized environment where it has been suggested that primitive metabolic activities might have originated.

RNA dominated primordial world: Two major well-accepted supporting facts

1. Investigators have produced a diverse array of ribozymes that catalyze fundamental metabolic reactions and bind specific ligands.
2. “molecular fossils” in extant metabolism.
3. Mathematical estimations show that simple activities such as binding to a metal ion or scaffold can potentially arise at very low concentrations (zeptomole) in the initial random pool of RNA oligomers.

How can DNA be a catalyst?

In vitro selection to identify catalytic DNA

• Like ribozymes, dRibozymes need to be single-stranded.
• Varying degrees of confirmations.
• Chemical synthesis of a random pool of DNA oligos attached to a constant region (10¹⁴ molecules).
• PCR amplification.
• Selection – ability to cleave RNA.
• Tightening the selection pressure – incubation temperature, Mg⁺⁺/NaCl concentration.

Arguments against DNA next hypothesis

• Just because one can create RNAzyme that can catalyze aldol condensation in the lab does not provide the proof for the DNA next hypothesis.
• DNA biosynthesis occurs in two stages: RNR reduces 2’OH group – not easily achievable, DNA polymerase links the monomers.
• RNRs use an unusual and energetically difficult reaction mechanism based on free-radical chemistry and the conserved spatial arrangement of two thiol groups at the active site.
• The distribution of catalytic RNA within extant metabolism, together with the difficult biochemistry of ribonucleotide reduction, implies that sophisticated proteins probably predate DNA.

Why protein next

• The synthesis of deoxyribonucleotides was probably not achievable under prebiotic conditions.
• Although it is possible to synthesize deoxyribonucleotide by “force” chemistry, probably that is not what happened in the prebiotic world.
• Required enzymatically catalyzed ribonucleotide reduction.
• The prebiotic syntheses of both ribonucleotides and amino acids can occur without catalysis from biological enzymes.
• RNR ribosome is very hard to obtain by SELEX.
• RNR enzymes, irrespective of their origin, have a highly conserved free radical mechanism.

Why DNA next

• If the RNA world used abiotically synthesized DNA, ribonucleotide reduction would initially be unnecessary.
• Ribozymes might have augmented their capabilities by using sulfur-containing peptides as cofactors.

Counter argument

• Prebiotic synthesis experiments indicate that deoxyribose was very rare.
• Sulfur-containing amino acids were too unstable to have attained “useful” concentrations.

Inadequacy of RNA World Hypothesis

Assumptions of the RNA world:

• Genes were selected from a pool of RNA accumulated through RNA self-replication (without catalytic proteins).
• Proteins were synthesized for catalysis according to the specification of genes.
• Acquisition of genetic information must precede the creation of proteins with catalytic functions.

Drawbacks:

• The capability of RNA for self-replication as shown in the lab may not be relevant.
• How did the first gene appear that encoded for a functional water-soluble globular protein in the RNA world?

GADV Hypothesis – the Origin of Life

• Proposed by Kenji Ikehara.
• Primitive protein – only 4 amino acids — [GADV].
• Water-soluble globular structures at a high probability.
• Enough to form all types of secondary structures ([A]: a-helix, [V]: b-sheet, [G]: b-turn), but also act as a catalyst [D].
• [GADV]n-proteins could catalyze the formation of peptide bonds at a high probability – not demonstrated.
• [GADV]-proteins could even synthesize similar [GADV] proteins at a high probability – not demonstrated.

What is genomics?

Epistasis

• A genetic interaction where one or more genes can modify the expression of another gene and therefore its phenotype.
• When the two genes are not alternate alleles of the same phenotype.

Pleiotropy

• A phenomenon that describes the effect of a single gene on multiple phenotypic traits.

Heterosis

• A genetic phenomenon that describes the effects of the improved or increased function of any biological quality due to selective breeding to generate offsprings that are genetically superior to their parents.

Nuclear genome

• Comprises approximately 3.235 X10⁹ bps DNA.
• Divided into 24 linear molecules.
• The shortest 48 X10⁶ bp in length: Chromosome 21.
• The longest 249 X10⁶ bp in length: Chromosome 1.
• These 24 chromosomes consist of 22 autosomes and the two sex chromosomes, X and Y.

Mitochondrial genome

• Is a circular DNA molecule of 16,569 base pairs, up to 10 copies of in mitochondria (T A Brown-2016).

Contents of the human genome

Protein-coding regions

• Some regions are expressed as non-protein-coding RNA.
• Other regions are targets of regulatory interactions.
• Dynamic components of genomes: Transposable elements, Retrotransposons, Transposons.

How do you map a genome?

• Genome mapping is used to identify and record the location of genes and the distances between genes on a chromosome. Genome mapping provided a critical starting point for the Human Genome Project.
• Identifying the key “landmarks”.
• Sequenced DNA fragments can be aligned to the genome map to aid with the assembly of the genome.

Different types of genome mapping

• There are two general types of genome mapping called genetic mapping and physical mapping.
• Both guide towards the location of a gene (or section of DNA) on a chromosome.
• But, they rely on very different information.

Genetic mapping

• Looks at how genetic information is shuffled between chromosomes or between different regions in the same chromosome during meiosis? (a type of cell division). A process called recombination or ‘crossing over’.

Physical mapping

• Simply looks at the distance between known DNA sequences.

Types of SNPs

Noncoding SNPs

• 5’ UTR
• 3’ UTR
• Introns
• Intergenic Regions
• Pseudogenes
• Regulatory: Splicing, Transcriptional regulation (promoter & TF binding sites), Translational regulation (initiation or termination), Regulatory miRNA target sites.

Coding SNPs

• Synonymous SNPs (third position variation)
• Replacement SNPs (change Amino acid): Functional SNPs (acceptable amino acid replacement), Non-functional SNPs (traits & diseases).

How do we figure out the function of each SNP?

• By looking at their location.
• Many SNPs do not affect phenotypes at all.
• A way to determine which SNPs are significant and which are not could be very useful.

What makes us uniquely human?

• Genome sequences from an extinct late Pleistocene hominin can be reliably recovered.
• The analysis of the Neandertal genome shows that they are likely to have had a role in the genetic ancestry of present-day humans outside of Africa.
• Identification of a number of genomic regions and genes as candidates for positive selection early in modern human history, for example, those involved in cognitive abilities and cranial morphology.
• Further analyses of the Neandertal genome as well as the genomes of other archaic hominins will generate additional hypotheses and provide further insights into the origins and early history of present-day humans.

What is multicellularity?

There is a fundamental difference in the architecture of multicellularity between many species.

• Multicellularity can arise in two different ways: Divided cells remain attached, Aggregation of unicellular individuals.
• Multicellularity can confer many advantages: Protection against predation, Attachment to substrates, Greater buffering capacity against changing environs.
• Cells can become specialized by differentiation over a period of time.

What is the Cropping principle?

• Predation resulted in diversity.
• The presence of herbivores creates more niches for plants.
• This in turn increases the diversity of plants (predators – prey).
• Diversity is determined by species interactions.

Where on Earth does the highest diversity occur?

• Rain Forests
• Coral Reefs
• Deep Ocean

What is predation?

An organism killing another organism for nutritional purposes.

What then is the ideal model organism?

• It should be extant and include both unicellular and multicellular organisms that are closely related and exist today.
• Green algae – Volvox, Chlamydomonas are well suited to studying the evolution of multicellularity.
• The ~50 species in this group display a diverse range of body sizes and degrees of specialization, including single-celled forms and colonial forms with and without cellular differentiation.
• Some extant species are living fossils whose basic body plans have changed little in the last 200 million years!
• This diversity makes the volvocine algae a uniquely useful model system for understanding the evolution of multicellularity.

Mechanism of Cluster Formation

They showed that cluster formation is not simply by aggregation through cell surface glycoproteins but by post-division adhesion – results in high genetic identity within clusters – decreased conflict between individual cells.

Snowflake yeast are also phenotypically stable

Snowflake yeast did not lose its ability to form snowflakes through 35 generations (no selection pressure applied).

Phylogenetic analysis serves two major objectives

Assigning Phylogeny

• To infer the evolutionary relationships between “taxonomic units” (entities such as genes, populations, species, etc.).

Character and rate analysis

• Understanding the survival and evolution of traits or a particular character of our interest.

Cladogenesis

is the splitting of an evolutionary lineage into two genetically independent lineages.

Anagenesis

is the change or changes occurring along an evolutionary lineage.

Two possible interpretations for a multifurcation (polytomy) in a tree

1. The polytomy represents the true sequence of events (hard polytomy), whereby an ancestral taxon gave rise to three or more descendant taxa simultaneously.
2. The polytomy represents a lack of resolution. The exact order of two or more bifurcations cannot be determined unambiguously with the available data (soft polytomy).

Tree balance

is a measure of the degree of symmetry of a rooted phylogenetic tree. It serves as an indication of the pattern of speciation events in the group of taxa under study.

Limitations of phylogeny

• The rate of evolution is always unique: Mutation rate, population size, generation time and strength of selection.
• Levels of similarity are not reflective of the evolutionary relationships.

Two mechanisms leading to the generation of analogous features (other than common ancestry)

Similar-looking traits may have independent origins – analogy

1. Convergence: Similarities arise from distinct features in different lineages – adaptation to similar environments or similar life strategy. Example: Selection for improved flight in birds, bats and insects.
2. Parallel Evolution: Separate modification of the same feature. Example: evolution of gliding mechanisms in different species – squirrels, foxes, marsupials, lemurs etc. – modification of the hind leg.

Types of homology

• Orthology: Similarity due to speciation.
• Paralogy: Similarity due to gene duplication.
• Ohnology: A special case of paralogy in which similarity is due to genome duplication.
• Xenology: Similarity due to horizontal gene transfer.
• Gametology: denotes the relationship between homologous genes on nonrecombining, opposite sex chromosomes.

What are the basic (assumed) properties of LUCA?

It had properties shared by all independently living organisms on Earth representing the modern-day universal homologies.

• The genetic code is based on DNA.
• The genetic code is expressed via RNA intermediates.
• The genetic code is expressed into proteins.
• Synthesis of lipids or carbohydrates are the result of protein enzymes.
• ATP is used as an energy intermediate.
• The cell is surrounded by a cellular membrane composed of a lipid bilayer.
• The cell multiplies by duplicating all its contents followed by cellular division.

There are three primary sources of genetic variation:

• Mutations. A single mutation can have a large effect, but in many cases, evolutionary change is based on the accumulation of many mutations.
• Gene flow is any movement of genes from one population to another and is an important source of genetic variation.
• Sex can introduce new gene combinations into a population. This genetic shuffling is another important source of genetic variation.

Red Queen Hypothesis

• Parasites are constantly evolving into new forms to avoid host resistance.
• Hosts are constantly under selective pressure to evolve new resistance genes.
• The result is a “coevolutionary arms race” in which both parasite and host must constantly evolve just to stay in place.

Mutualism – Important Concepts

• Mutualism is a relationship between two organisms where both of them benefit from the relationship.
• Interaction is consistent and sometimes constant.
• Both gain in fitness.
• This could involve providing food, protection, a place to live or even pollination.

Definition of a virus is influenced by the properties of cells!

1. Contain a single type of nucleic acid (RNA or DNA). Cells have the two kinds.
2. No Lipmann system (ATP generation). Cells must have one.
3. Ultimate parasite: use the host translation system. Cells must have a translation system.
4. No growth, no division. Cells do divide.
5. Eclipse phase in viruses. Cells never “disappear”.