Просмотр кода страницы Sequence space (evolution)

{{Short description|Representation of possible genetic sequences}}
[[File:Protein Sequence space.svg|thumb|600px|[[Protein]] sequence space can be represented as a space with n [[dimensions]], where n is the number of [[amino acid]]s in the protein. Each axis has 20 positions representing the 20 amino acids. There are 400 possible 2 amino acid proteins ([[dipeptide]]) which can be arranged in a 2D grid. the 8000 [[tripeptide]]s can be arranged in a 3D cube. Most proteins are longer than 100 amino acids and so occupy large, multidimensional spaces containing an astronomical number protein sequences.]]

[[File:DE landscape.png|thumb|How [[directed evolution]] climbs fitness landscapes. Performing multiple rounds of directed evolution is useful not only because a new library of mutants is created in each round, but also because each new library uses better mutants as templates than the previous. The experiment is analogous to climbing a hill on a 'fitness landscape,' where elevation represents the desired property. The goal is to reach the summit, which represents the best achievable mutant. Each round of selection samples mutants on all sides of the starting template (1) and selects the mutant with the highest elevation, thereby climbing the hill. This is repeated until a local summit is reached (2).]]

In [[evolutionary biology]], '''sequence space''' is a way of representing all possible sequences (for a [[protein]], [[gene]] or [[genome]]).<ref>{{cite journal|last=DePristo|first=Mark A.|author2=Weinreich, Daniel M. |author3=Hartl, Daniel L. |title=Missense meanderings in sequence space: a biophysical view of protein evolution|journal=Nature Reviews Genetics|date=2 August 2005|volume=6|issue=9|pages=678–687|doi=10.1038/nrg1672|pmid=16074985|s2cid=13236893}}</ref><ref>{{cite journal|last1=Maynard Smith|first1=John|title=Natural Selection and the Concept of a Protein Space|journal=Nature|date=7 February 1970|volume=225|issue=5232|pages=563–564|doi=10.1038/225563a0|pmid=5411867|bibcode=1970Natur.225..563M|s2cid=204994726}}</ref> The sequence space has one dimension per [[amino acid]] or [[nucleotide]] in the sequence leading to [[dimension|highly dimensional spaces]].<ref name=":0">{{cite journal|last=Bornberg-Bauer|first=E.|author2=Chan, H. S. |title=Modeling evolutionary landscapes: Mutational stability, topology, and superfunnels in sequence space|journal=Proceedings of the National Academy of Sciences|date=14 September 1999|volume=96|issue=19|pages=10689–10694|doi=10.1073/pnas.96.19.10689|pmid=10485887|pmc=17944|bibcode=1999PNAS...9610689B|doi-access=free}}</ref><ref name=":1">{{cite journal|last=Cordes|first=MH|author2=Davidson, AR |author3=Sauer, RT |title=Sequence space, folding and protein design.|journal=Current Opinion in Structural Biology|date=Feb 1996|volume=6|issue=1|pages=3–10|pmid=8696970|doi=10.1016/S0959-440X(96)80088-1}}</ref>

Most sequences in sequence space have no function, leaving relatively small regions that are populated by naturally occurring genes.<ref>{{cite journal|last=Hermes|first=JD|author2=Blacklow, SC |author3=Knowles, JR |title=Searching sequence space by definably random mutagenesis: improving the catalytic potency of an enzyme.|journal=Proceedings of the National Academy of Sciences of the United States of America|date=Jan 1990|volume=87|issue=2|pages=696–700|pmid=1967829|pmc=53332|doi=10.1073/pnas.87.2.696|bibcode=1990PNAS...87..696H|doi-access=free}}</ref> Each protein sequence is adjacent to all other sequences that can be reached through a single [[mutation]].<ref>{{Cite journal |last1=Romero |first1=Philip A. |last2=Arnold |first2=Frances H. |date=December 2009 |title=Exploring protein fitness landscapes by directed evolution |journal=Nature Reviews Molecular Cell Biology |language=en |volume=10 |issue=12 |pages=866–876 |doi=10.1038/nrm2805 |issn=1471-0080 |pmc=2997618 |pmid=19935669}}</ref> It has been estimated that the whole functional protein sequence space has been explored by life on the Earth.<ref>{{Cite journal|url=http://rsif.royalsocietypublishing.org/content/5/25/953|doi = 10.1098/rsif.2008.0085|title = How much of protein sequence space has been explored by life on Earth?|year = 2008|last1 = Dryden|first1 = David T.F|last2 = Thomson|first2 = Andrew R.|last3 = White|first3 = John H.|journal = Journal of the Royal Society Interface|volume = 5|issue = 25|pages = 953–956|pmid = 18426772|pmc = 2459213}}</ref> Evolution by natural selection can be visualised as the process of sampling nearby sequences in sequence space and moving to any with improved [[fitness (biology)|fitness]] over the current one.

==Representation==
A sequence space is usually laid out as a grid. For [[protein]] sequence spaces, each [[amino acid|residue]] in the protein is represented by a [[dimension]] with 20 possible positions along that axis corresponding to the possible amino acids.<ref name=":0" /><ref name=":1" /> Hence there are 400 possible [[dipeptide]]s arranged in a 20x20 space but that expands to 10<sup>130</sup> for even a small protein of 100 amino acids arranged in a space with 100 dimensions. Although such overwhelming multidimensionality cannot be visualised or represented diagrammatically, it provides a useful abstract model to think about the range of proteins and [[evolution]] from one sequence to another.

These highly multidimensional spaces can be compressed to 2 or 3 dimensions using [[principal component analysis]]. A fitness landscape is simply a sequence space with an extra vertical axis of fitness added for each sequence.<ref>{{cite journal|last=Romero|first=PA|author2=Arnold, FH |title=Exploring protein fitness landscapes by directed evolution.|journal=Nature Reviews Molecular Cell Biology|date=Dec 2009|volume=10|issue=12|pages=866–76|pmid=19935669|doi=10.1038/nrm2805|pmc=2997618}}</ref>

==Functional sequences in sequence space==
Despite the diversity of protein superfamilies, sequence space is extremely sparsely populated by functional proteins. Most random protein sequences have no fold or function.<ref>{{cite journal|last=Keefe|first=AD|author2=Szostak, JW |title=Functional proteins from a random-sequence library.|journal=Nature|date=Apr 5, 2001|volume=410|issue=6829|pages=715–8|pmid=11287961|doi=10.1038/35070613|pmc=4476321|bibcode=2001Natur.410..715K}}</ref> [[protein superfamily|Enzyme superfamilies]], therefore, exist as tiny clusters of active proteins in a vast empty space of non-functional sequence.<ref>{{cite journal|last=Stemmer|first=Willem P. C.|title=Searching Sequence Space|journal=Bio/Technology|date=June 1995|volume=13|issue=6|pages=549–553|doi=10.1038/nbt0695-549|s2cid=20117819}}</ref><ref>{{cite journal|last=Bornberg-Bauer|first=E|title=How are model protein structures distributed in sequence space?|journal=Biophysical Journal|date=Nov 1997|volume=73|issue=5|pages=2393–403|pmid=9370433|doi=10.1016/S0006-3495(97)78268-7|pmc=1181141|bibcode=1997BpJ....73.2393B}}</ref>

The density of functional proteins in sequence space, and the proximity of different functions to one another is a key determinant in understanding [[evolvability]].<ref>{{cite journal|last=Bornberg-Bauer|first=E|author2=Huylmans, AK |author3=Sikosek, T |title=How do new proteins arise?|journal=Current Opinion in Structural Biology|date=Jun 2010|volume=20|issue=3|pages=390–6|pmid=20347587|doi=10.1016/j.sbi.2010.02.005}}</ref> The degree of interpenetration of two [[neutral network (evolution)|neutral networks]] of different [[enzyme activity|activities]] in sequence space will determine how easy it is to evolve from one activity to another. The more overlap between different activities in sequence space, the more [[cryptic variation]] for [[promiscuous activity]] will be.<ref>{{cite book|last=Wagner|first=Andreas|title=The origins of evolutionary innovations : a theory of transformative change in living systems|publisher=Oxford University Press|location=Oxford [etc.]|isbn=978-0199692590|date=2011-07-14}}</ref>

Protein sequence space has been compared to the ''[[Library of Babel]]'', a theoretical library containing all possible books that are 410 pages long.<ref>{{cite journal|last1=Arnold|first1=FH|title=The Library of Maynard-Smith: My Search for Meaning in the protein universe|journal=Advances in Protein Chemistry|date=2000|volume=55|pages=ix–xi|pmid=11050930|doi=10.1016/s0065-3233(01)55000-7}}</ref><ref>{{cite journal|last1=Ostermeier|first1=M|title=Beyond cataloging the Library of Babel.|journal=Chemistry & Biology|date=March 2007|volume=14|issue=3|pages=237–8|pmid=17379136|doi=10.1016/j.chembiol.2007.03.002|doi-access=}}</ref> In the ''Library of Babel'', finding any book that made sense was impossible due to the sheer number and lack of order. The same would be true of protein sequences if it were not for natural selection, which has selected out only protein sequences that make sense. Additionally, each protein sequences is surrounded by a set of neighbours (point mutants) that are likely to have at least some function.

On the other hand, the effective "alphabet" of the sequence space may in fact be quite small, reducing the useful number of amino acids from 20 to a much lower number. For example, in an extremely simplified view, all amino acids can be sorted into two classes (hydrophobic/polar) by [[hydrophobicity]] and still allow many common structures to show up. Early life on Earth may have only four or five types of amino acids to work with,<ref>{{cite journal |last1=Dryden |first1=DT |last2=Thomson |first2=AR |last3=White |first3=JH |title=How much of protein sequence space has been explored by life on Earth? |journal=Journal of the Royal Society, Interface |date=6 August 2008 |volume=5 |issue=25 |pages=953–6 |doi=10.1098/rsif.2008.0085 |pmid=18426772 |pmc=2459213}}</ref> and researches have shown that functional proteins can be created from wild-type ones by a similar alphabet-reduction process.<ref>{{cite journal |last1=Akanuma |first1=S. |last2=Kigawa |first2=T. |last3=Yokoyama |first3=S. |title=Combinatorial mutagenesis to restrict amino acid usage in an enzyme to a reduced set |journal=Proceedings of the National Academy of Sciences |date=2 October 2002 |volume=99 |issue=21 |pages=13549–13553 |doi=10.1073/pnas.222243999 |pmid=12361984 |pmc=129711 |bibcode=2002PNAS...9913549A |doi-access=free}}</ref><ref>{{cite journal |last1=Fujishima |first1=Kosuke |last2=Wang |first2=Kendrick M. |last3=Palmer |first3=Jesse A. |last4=Abe |first4=Nozomi |last5=Nakahigashi |first5=Kenji |last6=Endy |first6=Drew |last7=Rothschild |first7=Lynn J. |author-link=Lynn J. Rothschild|title=Reconstruction of cysteine biosynthesis using engineered cysteine-free enzymes |journal=Scientific Reports |date=29 January 2018 |volume=8 |issue=1 |pages=1776 |doi=10.1038/s41598-018-19920-y |pmid=29379050 |pmc=5788988 |bibcode=2018NatSR...8.1776F |doi-access=free}}</ref> Reduced alphabets are also useful in [[bioinformatics]], as they provide an easy way of analyzing protein similarity.<ref>{{cite journal |last1=Bacardit |first1=Jaume |last2=Stout |first2=Michael |last3=Hirst |first3=Jonathan D |last4=Valencia |first4=Alfonso |last5=Smith |first5=Robert E |last6=Krasnogor |first6=Natalio |title=Automated Alphabet Reduction for Protein Datasets |journal=BMC Bioinformatics |date=6 January 2009 |volume=10 |issue=1 |pages=6 |doi=10.1186/1471-2105-10-6|pmid=19126227 |pmc=2646702 |doi-access=free }}</ref><ref>{{cite journal |last1=Solis |first1=Armando D. |title=Reduced alphabet of prebiotic amino acids optimally encodes the conformational space of diverse extant protein folds |journal=BMC Evolutionary Biology |date=30 July 2019 |volume=19 |issue=1 |doi=10.1186/s12862-019-1464-6|pmid=31362700 |doi-access=free |pmc=6668081 |article-number=158 |bibcode=2019BMCEE..19..158S }}</ref>

==Exploration through directed evolution and rational design==
{{main|Directed evolution}}
[[File:How random DNA libraries sample sequence space.pdf|thumb|How [[Library (biology)|DNA libraries]] generated by [[Mutagenesis (molecular biology technique)#Random mutagenesis|random mutagenesis]] sample sequence space. The amino acid substituted into a given position is shown. Each dot or set of connected dots is one member of the library. Error-prone PCR randomly mutates some residues to other amino acids. Alanine scanning replaces each reside of the protein with alanine, one-by-one. Site saturation substitutes each of the 20 possible amino acids (or some subset of them) at a single position, one-by-one.]]

A major focus in the field of [[protein engineering]] is on creating [[Library (biology)|DNA libraries]] that [[sampling (statistics)|sample]] regions of sequence space, often with the goal of finding mutants of proteins with enhanced functions compared to the [[wild type]]. These libraries are created either by using a wild type sequence as a template and applying one or more [[Mutagenesis (molecular biology technique)|mutagenesis]] techniques to make different variants of it, or by creating proteins from scratch using [[artificial gene synthesis]]. These libraries are then [[Protein engineering#Screening and selection techniques|screened or selected]], and ones with improved [[phenotype]]s are used for the next round of mutagenesis.

==See also==
* [[Protein]]
* [[Sequence space]]
* [[Directed evolution]]
* [[Protein engineering]]
* [[High-dimensional space]]

==References==
{{reflist|35em}}
{{genarch}}

[[Category:Evolutionary biology]]
[[Category:Genetics]]
[[Category:Biochemistry]]