Developmental noise

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Developmental noise or stochastic noise is a concept within developmental biology in which the observable characteristics or traits (phenotype) varies between individuals even though both individuals share the same genetic code (genotypes) and the other environmental factors are completely the same. [1] [2] Factors that influence the effect include stochastic, or randomized, gene expression and other cellular noise. [3]

Contents

Definition

Although organisms within a species share very similar genes, similar environments and similar developmental history, each individual organism can develop differences due to noise in signaling and signal interpretation. This developmental noise may help individuals gain the ability to adapt to the environment and contribute to their unique patterns of development. [4] Human fingerprints provide a well-known example; the fingerprints differ even between genetically identical human twins. [5]

Use of noise in biology

Developmental noise may help individuals gain the ability to adapt to the environment. Biological systems display both variation and robustness. [6] Natural variation within a population is in large part genetically determined, but variation due to noise may contribute to a rapid response by an individual to changes in the environment. This variation can have an evolutionary tuning effect that contributes to the optimal fitness of a population. In support of this idea, it has been shown that bacteria can switch stochastically into a "persistent" state which has slow growth coupled with an ability to survive antibiotic treatment. [7] In another study, it has been shown that most of the noisy proteins were associated with the stress response. When proteins are expressed in small quantities, the expression of more noisy proteins will be more influenced by noises which come from the environmental context. Types of noises include extrinsic noise which is the variation in cell-to-cell expression level of protein, and intrinsic noise which is the variation of the inherent stochastic nature of protein expression. [8] Moreover, noisy genes are associated with a distinct promoter architecture, including the prevalence of TATA boxes, consistent with the theoretical predictions that noise is greatly influenced by the logic of the transcriptional process itself and, in particular, the transition from closed to open chromatin. [9]

The developmental noise can contribute to unique patterns of development in each individual as well. During development of a complex organ, variability in gene expression may be required to contribute to differentiation of multiple cell types from cells that have equivalent potential. For example, the patterning of the adult fly eye relies on multiple alternative choices of differentiation pathways within an apparently homogeneous field of cells. The facets (ommatidia) in fly eyes occur as two types, designated pale and yellow, as defined by the particular types of rhodopsin photopigments expressed in the two inner photoreceptor cells. [10] [11] In flies carrying mutations in the gene spineless, all ommatidia show the pale fate, while over expression of spineless induces the yellow fate. The final pattern of ommatidia is determined by stochastic variation in expression of this single transcription factor Spineless. [10]

A comprehensive review article summarized effects of noise on cellular decisions from bacteria to mammalian cells. [12]

Developmental noise in plants

The majority of study on developmental noise has focused on animals, but there are also examples from plants. In one early study, Roy made thousands of observations on petal numbers as well as on leaf tooth numbers. He observed a high degree of variability in both traits. After analyzing his data, he could not conclude that the variability was caused by environmental effect. Another example of noise in plants is lateral root behavior. People found that the growth of lateral roots is unpredictable in genetically identical plants which grow in the same environment. One more example of seed germination may illustrate the benefit of developmental noise in plants. Stochasticity in the timing of germination ensures that at least a fraction of the progeny will survive to reproduce. [11]

Noise and robustness

Though stochastic variations in cell behaviors may be beneficial, most biological systems need to maintain a reliable output without unpredictable variations. This ability to buffer variations generated by molecular noise, genetic polymorphism, or environmental fluctuations is termed robustness.

For example, in the development of the repeating blocks of somites in the mesoderm of vertebrate animals, even though the biological system may be subject to a noisy environment, the segmentation clock maintains periodic gene expression through coupled oscillators, in which synchronous oscillation of neighbors is maintained through mutual coupling. This mechanism enables embryos to maintain a constant segregation of somites, despite the noise imposed by the high level mitosis required for continued growth. [13]

Further study

The sources, consequences, and control of noise are major questions in study of developmental noise. Recent studies suggest that this noise has multiple sources, including the stochastic or inherently random nature of the biochemical reactions of gene expression. But the detailed mechanisms are still unclear and the contributions of factors such as microRNAs, whose existence was first discovered in the 1990s, remain unclear. For example, one recent study showed that microRNAs can serve different roles, from using noise to throw a developmental switch to buffering the consequences of noise in order to confer robustness to environmental perturbation. [13] Thus, much work remains to be done in understanding the significance, control and mechanisms of developmental noise.

See also

Related Research Articles

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In genetics, the phenotype is the set of observable characteristics or traits of an organism. The term covers the organism's morphology, its developmental processes, its biochemical and physiological properties, its behavior, and the products of behavior. An organism's phenotype results from two basic factors: the expression of an organism's genetic code and the influence of environmental factors. Both factors may interact, further affecting the phenotype. When two or more clearly different phenotypes exist in the same population of a species, the species is called polymorphic. A well-documented example of polymorphism is Labrador Retriever coloring; while the coat color depends on many genes, it is clearly seen in the environment as yellow, black, and brown. Richard Dawkins in 1978 and then again in his 1982 book The Extended Phenotype suggested that one can regard bird nests and other built structures such as caddisfly larva cases and beaver dams as "extended phenotypes".

Nature versus nurture is a long-standing debate in biology and society about the relative influence on human beings of their genetic inheritance (nature) and the environmental conditions of their development (nurture). The alliterative expression "nature and nurture" in English has been in use since at least the Elizabethan period and goes back to medieval French. The complementary combination of the two concepts is an ancient concept. Nature is what people think of as pre-wiring and is influenced by genetic inheritance and other biological factors. Nurture is generally taken as the influence of external factors after conception e.g. the product of exposure, experience and learning on an individual.

<span class="mw-page-title-main">Gene regulatory network</span> Collection of molecular regulators

A generegulatory network (GRN) is a collection of molecular regulators that interact with each other and with other substances in the cell to govern the gene expression levels of mRNA and proteins which, in turn, determine the function of the cell. GRN also play a central role in morphogenesis, the creation of body structures, which in turn is central to evolutionary developmental biology (evo-devo).

<span class="mw-page-title-main">Protein isoform</span> Forms of a protein produced from different genes

A protein isoform, or "protein variant", is a member of a set of highly similar proteins that originate from a single gene or gene family and are the result of genetic differences. While many perform the same or similar biological roles, some isoforms have unique functions. A set of protein isoforms may be formed from alternative splicings, variable promoter usage, or other post-transcriptional modifications of a single gene; post-translational modifications are generally not considered. Through RNA splicing mechanisms, mRNA has the ability to select different protein-coding segments (exons) of a gene, or even different parts of exons from RNA to form different mRNA sequences. Each unique sequence produces a specific form of a protein.

<i>Drosophila</i> embryogenesis Embryogenesis of the fruit fly Drosophila, a popular model system

Drosophila embryogenesis, the process by which Drosophila embryos form, is a favorite model system for genetics and developmental biology. The study of its embryogenesis unlocked the century-long puzzle of how development was controlled, creating the field of evolutionary developmental biology. The small size, short generation time, and large brood size make it ideal for genetic studies. Transparent embryos facilitate developmental studies. Drosophila melanogaster was introduced into the field of genetic experiments by Thomas Hunt Morgan in 1909.

Evolvability is defined as the capacity of a system for adaptive evolution. Evolvability is the ability of a population of organisms to not merely generate genetic diversity, but to generate adaptive genetic diversity, and thereby evolve through natural selection.

<i>Caulobacter crescentus</i> Species of bacterium

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In genetics, expressivity is the degree to which a phenotype is expressed by individuals having a particular genotype. Alternatively, it may refer to the expression of a particular gene by individuals having a certain phenotype. Expressivity is related to the intensity of a given phenotype; it differs from penetrance, which refers to the proportion of individuals with a particular genotype that share the same phenotype.

<span class="mw-page-title-main">Gene–environment interaction</span> Response to the same environmental variation differently by different genotypes

Gene–environment interaction is when two different genotypes respond to environmental variation in different ways. A norm of reaction is a graph that shows the relationship between genes and environmental factors when phenotypic differences are continuous. They can help illustrate GxE interactions. When the norm of reaction is not parallel, as shown in the figure below, there is a gene by environment interaction. This indicates that each genotype responds to environmental variation in a different way. Environmental variation can be physical, chemical, biological, behavior patterns or life events.

<span class="mw-page-title-main">Copy number variation</span> Repeated DNA variation between individuals

Copy number variation (CNV) is a phenomenon in which sections of the genome are repeated and the number of repeats in the genome varies between individuals. Copy number variation is a type of structural variation: specifically, it is a type of duplication or deletion event that affects a considerable number of base pairs. Approximately two-thirds of the entire human genome may be composed of repeats and 4.8–9.5% of the human genome can be classified as copy number variations. In mammals, copy number variations play an important role in generating necessary variation in the population as well as disease phenotype.

<span class="mw-page-title-main">Canalisation (genetics)</span> Measure of the ability of a population to produce the same phenotype

Canalisation is a measure of the ability of a population to produce the same phenotype regardless of variability of its environment or genotype. It is a form of evolutionary robustness. The term was coined in 1942 by C. H. Waddington to capture the fact that "developmental reactions, as they occur in organisms submitted to natural selection...are adjusted so as to bring about one definite end-result regardless of minor variations in conditions during the course of the reaction". He used this word rather than robustness to consider that biological systems are not robust in quite the same way as, for example, engineered systems.

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Transcriptional bursting, also known as transcriptional pulsing, is a fundamental property of genes in which transcription from DNA to RNA can occur in "bursts" or "pulses", which has been observed in diverse organisms, from bacteria to mammals.

Transcriptional noise is a primary cause of the variability (noise) in gene expression occurring between cells in isogenic populations. A proposed source of transcriptional noise is transcriptional bursting although other sources of heterogeneity, such as unequal separation of cell contents at mitosis are also likely to contribute considerably. Bursting transcription, as opposed to simple probabilistic models of transcription, reflects multiple states of gene activity, with fluctuations between states separated by irregular intervals, generating uneven protein expression between cells. Noise in gene expression can have tremendous consequences on cell behaviour, and must be mitigated or integrated. In certain contexts, such as establishment of viral latency, the survival of microbes in rapidly changing stressful environments, or several types of scattered differentiation, the variability may be essential. Variability also impacts upon the effectiveness of clinical treatment, with resistance of bacteria and yeast to antibiotics demonstrably caused by non-genetic differences. Variability in gene expression may also contribute to resistance of sub-populations of cancer cells to chemotherapy and appears to be a barrier to curing HIV.

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References

  1. ↑ Yampolsky LY, Scheiner SR (1994). "Developmental Noise, Phenotypic Plasticity, and Allozyme Heterozygosity in Daphnia". Evolution. 48 (5): 1715–22. doi:10.2307/2410259. JSTOR   2410259. PMID   28568411.
  2. ↑ Kærn, Mads; Elston, Timothy C.; Blake, William J.; Collins, James J. (June 2005). "Stochasticity in gene expression: from theories to phenotypes". Nature Reviews Genetics. 6 (6): 451–464. doi:10.1038/nrg1615. ISSN   1471-0064. PMID   15883588. S2CID   1028111.
  3. ↑ Horikawa K, Ishimatsu K, Yoshimoto E, Kondo S, Takeda H (June 2006). "Noise-resistant and synchronized oscillation of the segmentation clock". Nature. 441 (7094): 719–23. Bibcode:2006Natur.441..719H. doi:10.1038/nature04861. PMID   16760970. S2CID   4372075.
  4. ↑ Raser, J. M.; O'Shea, E. K. (2005). "Noise in gene expression: origins, consequences, and control". Science . 309 (5743): 2010–2013. Bibcode:2005Sci...309.2010R. doi:10.1126/science.1105891. PMC   1360161 . PMID   16179466.
  5. ↑ "Do identical twins have identical fingerprints?". Washington State Twin Registry. 1 October 2015. Retrieved 29 September 2019.
  6. ↑ Barkai, N.; Shilo, B. Z. (2007). "Variability and robustness in biomolecular systems". Mol Cell. 28 (5): 755–760. doi: 10.1016/j.molcel.2007.11.013 . PMID   18082601.
  7. ↑ Kussell, E.; Kishony, R.; Balaban, N. Q.; Leibler, S. (2005). "Bacterial persistence: a model of survival in changing environments". Genetics. 169 (4): 1807–1814. doi:10.1534/genetics.104.035352. PMC   1449587 . PMID   15687275.
  8. ↑ Chapman-McQuiston, E. (2007). The Effect of Noisy Protein Expression on E. coli/Phage Dynamics (Thesis).
  9. ↑ Blake, W. J.; et al. (2006). "Phenotypic consequences of promoter-mediated transcriptional noise". Mol Cell. 24 (6): 853–865. doi: 10.1016/j.molcel.2006.11.003 . PMID   17189188.
  10. 1 2 Wernet, M. F.; et al. (2006). "Stochastic spineless expression creates the retinal mosaic for colour vision". Nature . 440 (7081): 174–180. Bibcode:2006Natur.440..174W. doi:10.1038/nature04615. PMC   3826883 . PMID   16525464.
  11. 1 2 Forde, B. G. (2009). "Is it good noise? The role of developmental instability in the shaping of a root system". J Exp Bot. 60 (14): 3989–4002. doi: 10.1093/jxb/erp265 . PMID   19759097.
  12. ↑ Balázsi, Gábor; van Oudenaarden, Alexander; Collins, James J (2011). "Cellular Decision Making and Biological Noise: From Microbes to Mammals". Cell. 144 (6): 910–925. doi:10.1016/j.cell.2011.01.030. PMC   3068611 . PMID   21414483.
  13. 1 2 Ishimatsu, K.; Horikawa, K.; Takeda, H. (2007). "Coupling cellular oscillators: a mechanism that maintains synchrony against developmental noise in the segmentation clock". Dev Dyn. 236 (6): 1416–1421. doi: 10.1002/dvdy.21139 . PMID   17420984.
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