G-value Paradox
   HOME

TheInfoList



OR:

The G-value paradox arises from the lack of correlation between the number of
protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respo ...
-coding
genes In biology, the word gene (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a ba ...
among
eukaryotes Eukaryotes () are organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the three domains of life. Bacte ...
and their relative biological complexity. The microscopic
nematode The nematodes ( or grc-gre, Νηματώδη; la, Nematoda) or roundworms constitute the phylum Nematoda (also called Nemathelminthes), with plant-Parasitism, parasitic nematodes also known as eelworms. They are a diverse animal phylum inhab ...
''
Caenorhabditis elegans ''Caenorhabditis elegans'' () is a free-living transparent nematode about 1 mm in length that lives in temperate soil environments. It is the type species of its genus. The name is a blend of the Greek ''caeno-'' (recent), ''rhabditis'' (ro ...
'', for example, is composed of only a thousand cells but has about the same number of genes as a human. Researchers suggest resolution of the paradox may lie in mechanisms such as
alternative splicing Alternative splicing, or alternative RNA splicing, or differential splicing, is an alternative splicing process during gene expression that allows a single gene to code for multiple proteins. In this process, particular exons of a gene may be ...
and complex
gene regulation Regulation of gene expression, or gene regulation, includes a wide range of mechanisms that are used by cells to increase or decrease the production of specific gene products (protein or RNA). Sophisticated programs of gene expression are wi ...
that make the genes of humans and other complex eukaryotes relatively more productive.


DNA and biological complexity

The lack of correlation between the morphological complexity of eukaryotes and the amount of genetic information they carry has long puzzled researchers. The sheer amount of DNA in an organism, measured by the mass of DNA present in the
nucleus Nucleus ( : nuclei) is a Latin word for the seed inside a fruit. It most often refers to: *Atomic nucleus, the very dense central region of an atom *Cell nucleus, a central organelle of a eukaryotic cell, containing most of the cell's DNA Nucle ...
or the number of constituent
nucleotide Nucleotides are organic molecules consisting of a nucleoside and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecules wi ...
pairs, varies by several orders of magnitude among eukaryotes and often is unrelated to an organism’s size or developmental complexity. One
amoeba An amoeba (; less commonly spelled ameba or amœba; plural ''am(o)ebas'' or ''am(o)ebae'' ), often called an amoeboid, is a type of Cell (biology), cell or unicellular organism with the ability to alter its shape, primarily by extending and ret ...
has 200 times more DNA per cell than humans, and even insects and plants within the same
genus Genus ( plural genera ) is a taxonomic rank used in the biological classification of extant taxon, living and fossil organisms as well as Virus classification#ICTV classification, viruses. In the hierarchy of biological classification, genus com ...
can vary dramatically in their quantity of DNA. This
C-value C-value is the amount, in picograms, of DNA contained within a haploid nucleus (e.g. a gamete) or one half the amount in a diploid somatic cell of a eukaryotic organism. In some cases (notably among diploid organisms), the terms C-value and geno ...
paradox troubled genome scientists for many years. Eventually, researchers recognized that not all DNA contributes directly to the production of proteins and other biological functions.
Susumu Ohno Susumu is a masculine Japanese given name. Notable people with the name include: * Susumu Akagi (born 1972) Japanese voice actor *Susumu Aoyagi (青柳 進, born 1968), Japanese baseball player *Susumu Chiba (born 1970), Japanese voice actor *, Ja ...
coined the phrase “
junk DNA Non-coding DNA (ncDNA) sequences are components of an organism's DNA that do not genetic code, encode protein sequences. Some non-coding DNA is Transcription (genetics), transcribed into functional non-coding RNA molecules (e.g. transfer RNA, micro ...
” to describe these nonfunctional swaths of DNA. They include
introns An intron is any nucleotide sequence within a gene that is not expressed or operative in the final RNA product. The word ''intron'' is derived from the term ''intragenic region'', i.e. a region inside a gene."The notion of the cistron .e., gene. ...
, genetic sequences that are removed after
transcription Transcription refers to the process of converting sounds (voice, music etc.) into letters or musical notes, or producing a copy of something in another medium, including: Genetics * Transcription (biology), the copying of DNA into RNA, the fir ...
into
mRNA In molecular biology, messenger ribonucleic acid (mRNA) is a single-stranded molecule of RNA that corresponds to the genetic sequence of a gene, and is read by a ribosome in the process of Protein biosynthesis, synthesizing a protein. mRNA is ...
and thus are not
translated Translation is the communication of the meaning of a source-language text by means of an equivalent target-language text. The English language draws a terminological distinction (which does not exist in every language) between ''transla ...
into proteins;
transposable elements A transposable element (TE, transposon, or jumping gene) is a nucleic acid sequence in DNA that can change its position within a genome, sometimes creating or reversing mutations and altering the cell's genetic identity and genome size. Trans ...
that are mobile fragments of DNA, most of which are nonfunctional in humans; and
pseudogenes Pseudogenes are nonfunctional segments of DNA that resemble functional genes. Most arise as superfluous copies of functional genes, either directly by DNA duplication or indirectly by reverse transcription of an mRNA transcript. Pseudogenes are ...
, nonfunctional DNA sequences that originated from functional genes. The share of the human genome that may be considered “junk” remains controversial. Estimates reach as low as 8% and as high as 80%, with one researcher arguing that there is a fixed ceiling of 15% imposed by the genome’s
genetic load Genetic load is the difference between the fitness of an average genotype in a population and the fitness of some reference genotype, which may be either the best present in a population, or may be the theoretically optimal genotype. The average i ...
. (
Prokaryotes A prokaryote () is a single-celled organism that lacks a nucleus and other membrane-bound organelles. The word ''prokaryote'' comes from the Greek πρό (, 'before') and κάρυον (, 'nut' or 'kernel').Campbell, N. "Biology:Concepts & Connec ...
, which have little "junk" DNA by comparison, exhibit a fairly close relationship between genome size and biological functionality). In any case, the assumption was that once the C-paradox was swept away and the focus shifted to the number of protein-coding genes, the anticipated correlation between genetic information and biological complexity in eukaryotes would emerge. Unfortunately, the G-value paradox simply picked up where the C-value paradox left off, because the discrepancy persisted when comparisons were narrowed to just protein-coding genes.


G-value paradox

Estimates of the number of coding genes in the human
genome In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding ge ...
reached upwards of 100,000 prior to the
human genome project The Human Genome Project (HGP) was an international scientific research project with the goal of determining the base pairs that make up human DNA, and of identifying, mapping and sequencing all of the genes of the human genome from both a ...
, but since have dwindled to as low as 19,000 following completion of that massive
sequencing In genetics and biochemistry, sequencing means to determine the primary structure (sometimes incorrectly called the primary sequence) of an unbranched biopolymer. Sequencing results in a symbolic linear depiction known as a sequence which succ ...
effort and subsequent refinements. By comparison, the microscopic water flea
Daphnia pulex ''Daphnia pulex'' is the most common species of water flea. It has a cosmopolitan distribution: the species is found throughout the Americas, Europe, and Australia. It is a model species, and was the first crustacean to have its genome sequenced. ...
has about 31,000 genes; the nematode ''C. elegans'' about 19,700; the fruit fly ''(
Drosophila melanogaster ''Drosophila melanogaster'' is a species of fly (the taxonomic order Diptera) in the family Drosophilidae. The species is often referred to as the fruit fly or lesser fruit fly, or less commonly the "vinegar fly" or "pomace fly". Starting with Ch ...
)'' about 14,000; the zebrafish (''
Danio rerio The zebrafish (''Danio rerio'') is a freshwater fish belonging to the minnow family (Cyprinidae) of the order Cypriniformes. Native to South Asia, it is a popular aquarium fish, frequently sold under the trade name zebra danio (and thus often ...
),'' 26,000; and the small flowering plant ''Arabidopsis'' ''thaliana'''','' 27,000. Plants in general tend to have more genes than other eukaryotes. One explanation is their higher incidence of gene and whole genome duplication and retention of those additional genes, due in part to their development of a large collection of defensive
secondary metabolites Secondary metabolites, also called specialised metabolites, toxins, secondary products, or natural products, are organic compounds produced by any lifeform, e.g. bacteria, fungi, animals, or plants, which are not directly involved in the nor ...
. The apparent disconnect between the number of genes in a species and its biological complexity was dubbed the G-value paradox. While the C-value paradox unraveled with the discovery of massive sequences of noncoding DNA, resolution of the G-value paradox appears to rest on differences in genome productivity. Humans and other complex eukaryotes simply may be able to more with what they have, genetically speaking. Among the mechanisms cited for this greater productivity are more sophisticated transcriptional controls, multifunctional proteins, more interaction between protein products, alternative splicing and
post-translational modifications Post-translational modification (PTM) is the covalent and generally enzymatic modification of proteins following protein biosynthesis. This process occurs in the endoplasmic reticulum and the golgi apparatus. Proteins are synthesized by ribosomes ...
that may produce several protein products from the same genetic raw material. In addition, thousands of
non-coding RNAs A non-coding RNA (ncRNA) is a functional RNA molecule that is not translated into a protein. The DNA sequence from which a functional non-coding RNA is transcribed is often called an RNA gene. Abundant and functionally important types of non- ...
that are transcribed from DNA but not translated into protein have emerged as important regulators of gene expression and development in humans and other eukaryotes. They include short RNA sequences, such as
microRNAs MicroRNA (miRNA) are small, single-stranded, non-coding RNA molecules containing 21 to 23 nucleotides. Found in plants, animals and some viruses, miRNAs are involved in RNA silencing and post-transcriptional regulation of gene expression. miR ...
(miRNAs), small interfering RNAs (siRNAs) and Piwi-interacting RNAs (piRNAs), and long, non-coding RNAs (lncRNA) that may regulate gene expression at different stages of development. Some researchers suggest that instead of the number of genes the focus now should shift to gene interactions and the network of genetic regulatory mechanisms that allow them to support a variety of biological activities. These transitions have taken analysis of genetic complexity from the C-value to the G-value to what some refer to as the I-value, a measure of the total information contained in a genome.


Defining complexity

One of the challenges in the long debate over the mismatch between genome size and biological complexity has been ambiguity in defining complexity. Is it the number of
cell types A cell type is a classification used to identify cells that share morphological or phenotypical features. A multicellular organism may contain cells of a number of widely differing and specialized cell types, such as muscle cells and skin cells, ...
in an organism, the sophistication of its
nervous system In biology, the nervous system is the highly complex part of an animal that coordinates its actions and sensory information by transmitting signals to and from different parts of its body. The nervous system detects environmental changes th ...
or the number of different proteins it produces? By some definitions, the greater complexity of humans compared to other organisms may be illusory. Even once complexity is defined, some researchers argue complexity in function does not necessarily require the same complexity in process. Evolution is not a paragon of efficiency but travels a crooked path that leads to a more cumbersome genome than is necessary in some species.


References

{{Reflist Genomics