Transcription factors and evolution: An integral part of gene expression (Review) (2024)

1. Introduction

Understanding evolution requires the elucidation ofthe mechanisms through which phenotypic variation is generated andits subsequent consequences. In early studies of genetics, geneswere considered as trait-causing elements that are linearly arrayedon chromosomes (1). Extensivestudies on developmental biology, though, have implied that avariety of elements control the actions of genes, and these actionscan subsequently be altered (2,3).It is now accepted that various elements regulate the actions ofgenes and, subsequently, phenotypic variation. Therefore, themanner in which gene information is expressed has become animportant scientific topic. Gene expression is defined as a processthrough which the information encoded in a gene is used to directthe synthesis of a functional gene product (4). As a process, it may explain whyorganisms containing mostly the same DNA exhibit different celltypes and functions (5). Geneexpression is an intricate process and involves the coordination ofmultiple dynamic events, which are subject to multi-levelregulation (6). Those regulatorylevels include the transcriptional level, the post-transcriptionallevel, the translational level and the post-translational level.Regulating gene expression is crucial in living organisms (7). Gene regulation is essential incellular differentiation in multicellular organisms, since it cancontribute to the function and the structure of a specific cell,and is an integral part of organism development (4).

All of the above prove that apart from inheritedgenetic information, cell function and structure are influenced byinformation that is not encoded in the DNA sequence. Thisinformation has also been termed epigenetic information (5). Epigenetics is defined as bothheritable alterations in gene activity and expression and alsostable, long-term alterations in the transcriptional potential of acell that may not be heritable (8). Epigenetics comprises of a number ofmechanisms, which include DNA methylation, histone modification,post-translation modifications, chromatin remodeling and variousforms of regulatory RNA molecules. These mechanisms seem toinfluence gene expression (5).

Gene transcriptional regulation is a fundamentalpart of both tissue-specific gene expression and gene activity inresponse to stimuli (9). The mainregulators of gene transcription are transcription factors (TFs).TFs are defined as proteins that can bind specific DNA sequences tocontrol transcription (10). Eachcellular life form follows different strategies for the initiationand regulation of transcription. Prokaryotes use a single RNApolymerase, while eukaryotes exhibit multiple specialized RNApolymerases (11). Bacteria havetwo distinct mechanisms for the initiation of transcription, thepromoter-centric mechanism, in which specific TFs interact with thepromoter in order to alter its ability to bind RNA polymerase orRNA-centric mechanism, in which TFs interact with RNA in order toalter its promoter preference (12). In eukaryotes, a number of TFsinteract with their cognate DNA motifs and recruit transcriptionalcofactors to alter the chromatin environment. These TFs can alsofacilitate the assembly of a pre-initiation complex (PIC), which iscomposed of general TFs (GTFs) and RNA polymerase II (13). Lastly, the archaea transcriptionalmechanism can be summarized as a simplified version of theeukaryotic transcriptional mechanism (14). Archaea feature a transcriptionalapparatus that includes additional RNA polymerase subunits andbasal TFs that direct transcription initiation and elongation. TFsin the case of archaea recruit the RNA polymerase to the specificDNA domain.

The above underline the importance of TFs in boththe initiation and regulation of gene transcription. The activationof TFs is quite complex and may involve multiple intracellulartransduction pathways or direct activation through specificmolecules that bind, known as ligands (15). TFs mostly regulate gene activityby binding to specific short DNA base pair patterns termed motifsor cis-regulatory elements (CREs) in upstream, intron, ordownstream regions of target genes. They can also act byinteracting with other genomic locations that may be distant to theprimary DNA sequence (16). Theseare defined as gene regulatory regions. (17) CREs include promoters and sequencescalled enhancers in cases of transcriptional activation andsilencers in cases of transcriptional repression (18). The specific domain TFs have thatcan bind DNA is termed DNA binding domain (DBD). TFs use a varietyof DNA-binding structural motifs to recognize their targetsequences, which include homeodomain (HD), helix-turn-helix (HTH)and high-mobility group box (HMG). Such DBDs can be used toclassify TFs. The interaction between DNA and TFs goes beyond thestructural and sequence level since several other factorsparticipate in the process, such as the influence of cofactors,epigenetic modifications and the cooperative binding of other TFs(19). Thus, gene regulationinvolves a large number of molecular mechanisms. Therefore, anin-depth examination of the evolution of TFs, which takes intoaccount the interaction with all the molecular factors mentionedabove, and the manner through which TFs influence the evolution ofother molecular mediators, is essential to the understanding oforganism evolution.

2. Transcription factor evolution amongstlife domains

TF function involves two basic features: i) Theability to recognize and bind short, specific sequences of DNAwithin regulatory regions; and ii) the ability to recruit or bindproteins that participate in transcriptional regulation (20). Consequently, the evolution of TFsmainly depends on alterations in binding sites, binding partnersand expression patterns (10).Moreover, as an integral part of gene expression, they are closelyrelated to the evolution of epigenetic mechanisms (5). The current literature on TFevolution provides a broad range of information. Firstly, geneduplication and gene loss as crucial drivers of evolution (21,22) are subsequently important driversof TF evolution. Regardless of organism complexity, they arepresent in all domains of life. Duplication and deletion caninfluence transcriptional regulatory networks by increasing orreducing the number of TFs with specific binding preferences(23,24). Following the duplication of a TFgene, the two resulting gene copies are likely the same. Since theyshare the same sequence, including the DBD sequence, they bind tothe same target genes. Ensuing mutations in the DNA binding domainsequence can lead to one of the TF copies to switch to regulatingdifferent target genes. On a more lineage-specific level, TFsdisplay several differences. Although the basal transcriptionmachinery has long been considered universally conserved, it iscurrently accepted that it too diversifies during evolution. Thesize and subunit composition of the basal transcription machineryincrease highly during evolution, consisting of roughly 6 subunitsin bacteria, up to 15 in the archaea, and a large number ineukaryotes, which have at least 3 different RNA polymerases(25). Significant differencesare apparent between prokaryotes and eukaryotes. Firstly, some DBDsare specific to evolutionary lineages; e.g., the ribbon-helix-helixdomain is specific to bacteria and archaea while C2H2-ZNfs,Homeobox box, and T-box domains are specific to eukaryotes(26). Moreover, eukaryotic TFsare relatively longer than other eukaryotic proteins with adifferent function, while this association is reversed inprokaryotes. This phenomenon may be due to the fact that eukaryoticTFs have a number of long intrinsic disordered segments that areneeded to leverage the formation of a multi-protein transcriptionprotein complex (27). Anothercharacteristic specific to eukaryotes are the repeats of the sameDBD family in one polypeptide chain. This characteristic may be theresult of a mechanism eukaryotes use that increases the length anddiversity of DNA binding recognition sequences using a limitednumber of DNA binding domain families (27).

3. cis-Regulatory elements

Changes in CREs may influence TF evolution andfunction and vice versa (28,29). TFs can bind a single DNA bindingsite or full promoter/enhancer/silencer regions that featuremultiple binding sites. Several factors seem to affect theevolution, emergence, disappearance and function of CREs. Thesefactors include insertion and deletion mutational mechanisms,slippage processes, tje large rearrangement of promoter regions,co-operation amongst TFs and the existence of initial sequencedistributions that are biased towards the mutational neighborhoodof strongly binding sequences (30,31). Insertion and deletion mutationalmechanisms can lead to the slow emergence of binding sites out of arandom sequence, while factors that accelerate these processes mayinclude the already sufficient genomic sequence from which sitescan evolve and the possible co-operativity between adjacent TFs(30). Furthermore, since theinteraction of TFs' with TF binding sites is integral in generegulation, a mutation in either TF or binding site hinders thatinteraction and may lead to dysfunctional gene expression.Therefore, in order to maintain proper gene expression levels, TFevolution and CREs evolution are closely intertwined (32). They specifically bear aco-evolutionary association, where in order to sustain properinteraction, a mutation in one interacting partner could becompensated by a corresponding mutation in its' interacting partnerduring the course of evolution (32).

4. Co-operation among transcriptionfactors

Although prokaryote individual TFs can recognizelong DNA motifs that are alone capable of defining the genes theymay regulate, organisms with larger genomes are characterized byTFs that recognize sequences too short to be able to define uniquegenomic positions. Moreover, the development of multicellularorganisms requires molecular systems that are complex and able toexecute combinational processes. In an effort to overcome theseobstacles, organisms have evolutionary developed co-operativerecognition of DNA by multiple TFs (33). TFs can collaborate through avariety of mechanisms, with each co-operative mechanism determiningthe specifics of the regulatory interaction. Some of the mechanismsthrough which TFs cooperate include protein-protein interaction andindirect co-operation (33). Aprime example of protein-protein interaction among TFs is theformation of functional dimers. A number of eukaryotic TFs proteinsare not able to bind DNA sequences as monomeric proteins andrequire physical interaction with an identical molecule or onewithin the same family to form functional dimers that are able tobind targeted DNA sequences. It has been suggested that, at first,TFs function as monomers, something supported by the fact that TFsin less complex organisms can sufficiently bind target sequences asmonomers (34). Several promotersthat include symmetrical palindromic repeats of the DNA-recognitionmotif could have potentially brought two or more copies of the sameTF protein into proximity. If, by chance, an interaction domainwith only one interaction sequence appeared, then this would helpestablish the formation of a TF complex on DNA because thisspecific complex would recognize a larger DNA motif (34). These events would lead to morerelaxed evolutionary constraints on the TF DBD within a redundantduplicate gene and would allow the emergence of a DNA-bindingdomain that binds with less affinity, but is still functional. Oncesuch evolutionary steps are taken, the TF must function as anobligate dimer. Consequently, further duplication and changes inspecificity gave rise to the appearance and diversification of thevarious TFs' dimerizing families (34). The Co-operative binding of TFs toDNA can also occur without direct protein-protein interactions.This co-operation is achieved through a process known as indirectco-operativity or collaborative competition, in which a cohort ofTFs collectively competes with the same histone octamer for accessto the underlying DNA (35).Collaborative competition arises automatically from the closejuxtaposition of binding sites for arbitrarily chosen TFs (36). Therefore, collaborativecompetition may play an important role in the evolution of generegulatory modules, since molecules that undergo combinatorialregulation may be assembled from randomly selected components, withno requirement for coevolution. Following the coevolution of therequired partners can increase the co-operativity through theaforementioned protein-protein contacts or bridging proteins, andmay thus increase the magnitude of combinational control (36).

5. Transcriptional cofactors andpost-translational modifications

A number of co-activator and co-repressor proteinsare components of multi-subunit coregulator complexes that exhibitdiverse enzymatic activities (37). Specifically, TF activity isregulated via post-translational modifications (PTMs) by suchmodification enzymes as a response to cellular stimuli (38). Modification enzymes directlyinteract with TFs and modify specific residues of the TF proteinand alter subcellular localization, stability, interaction withmore cofactors and other transcriptional activities (39). Some of the modifications thoseenzymes undertake are phosphorylation, acetylation, methylation andglycosylation (38). It is,therefore, likely that PTMs of histones, TFs, or polymerase II andits associated proteins at the PIC are involved inenhancer-core-promoter communication and potentially, in thecombinatorial regulation of transcription activation (40). Thus, it is not unexpected thatrecent research has demonstrated connections between novel PTMssites within TFs and the evolution of new features (20). A prime example is the evolution ofpregnancy in mammals, in which amino-acid changes in the TFCCAAT/enhancer-binding protein beta (CEBPB) change the manner inwhich it responds to cyclic AMP/protein kinase A (cAMP/PKA)signaling (41). Such amino-acidchanges reorganize the location of key phosphorylation sites andmay change the response of CEBPB to phosphorylation from repressionto activation (41).

6. Transcription factors and theirexpression patterns

TFs in eukaryotes are functionally divergent betweendifferent species and paralogs, which proves that they can evolvenew functions (42). Ineukaryotes, 5 groups of TFs with distinct expression patterns haveemerged through periodic expansion in the TF repertoire. Theseinclude groups that are present only in primates, those that aregenerally found in mammals, vertebrates, or metazoan and thosefound in most eukaryotes, including yeast (43). A mechanism that can drive suchevolutionary alterations in TF function is tissue-specific geneexpression (42). Tissue-specificgene expression as a mechanism can enhance the specificity of TFsthrough minimizing the pleiotropic effects of mutations that couldlead to the gain of novel regulatory links via TF evolution, whilesimultaneously restricting the effects of loss of functionmutations that break important regulatory links (42). A more thorough understanding ofthe association between TFs and tissue specificity can be achievedby studying the expansions that occur in the TF repertoire inconjunction with the evolution of tissue-specific mechanisms. Theexpansions mentioned above seem to have occurred unevenly for TFscontaining different types of DNA-binding domains. Some DBDs haveexpanded rapidly through evolution, while others have not expandedsignificantly since their emergence. These expansions could haveprovided evolution with the means through which to modify or createdifferent expression patterns for transcriptional factors,including tissue-specific ones, by duplication followed by promoterdivergence (43).

7. Transcription factors and histonemodifications

Human cell DNA is wrapped around histone proteinoctamers. This protein complex is known as the ‘nucleosomal coreparticle’ (44). Histone proteinshave tails which include residues that can be post-translationallymodified and influence transcription. This effect on transcriptionis regulated by changes in histone modification patterns thatsurround TF binding motifs (45).It is speculated that TFs with evolutionary related DNA bindingdomains sample putative binding sites with similar histonemodification pattern environments (45).

8. Transcription factors and miRNAs

MicroRNAs (miRNAs or miRs) are small regulatorynon-coding RNAs that influence gene regulation (46). Along with TFs, they play animportant role in gene regulatory network evolution (47). It seems that gene expression ismainly regulated by TFs at the transcriptional level and miRNA atthe post-transcriptional level, with both expression regulatorshaving the ability to regulate each other. The interplay betweenTFs and miRNAs provides specific constraints and innovations forthe evolution of such networks. It is thus expected that they alsoexhibit some form of coevolution. Coevolution seems to exist in TFand miRNAs pairs that are connected by transcriptional activationsignals but not in pairs that are connected by transcriptionalrepression signals (48). Thisassociation may be explained by the fact that TFs that triggermiRNA expression can subsequently function together with theactivated miRNAs, while TFs that repress the expression of specificmiRNAs will not function with them later and thus be under theirevolutionary influence (48).

9. Ligand-dependent transcription factors:The case of nuclear receptors

As it has been already stated, a number oftranscriptional factors may be activated through ligand binding. Insuch cases, ligands are essential to TF function and are expectedto be an integral part of their evolution. Prime examples ofligand-dependent TFs are nuclear receptors (NRs), which modulategene transcription in direct response to small lipophilic molecules(49). Apart from thecharacteristic DBD of all TFs, NRs feature a structural domain thatbinds ligands, termed ligand-binding domain (LBD). Ligand bindinginduces a conformational change that activates the receptor andstimulates the activity of its' target gene (50). NR ligands are productintermediates of various metabolic pathways. This fact means thatthey have been evolutionary established through genetic modulationson the components of particular metabolic pathways but not throughmodification of a single gene. Consequently, this fact indicatesthat NR evolution is heavily influenced not only by selective genesbut by the ever-expanding interaction among gene networks (51).

10. Conclusions

Studying the evolution of developmental processes isessential in shedding light on how morphological diversity emerged(52). TFs have a major role inmulticellular eukaryotes development, and they are the mainregulators of embryonic development in embryophytes and metazoans(53). This role is expectedsince development is controlled mainly by gene regulatory networks,which in turn are controlled by TFs (52). TFs appear to regulate up tohundreds of genes that are related to organism development and hintat the existence of vast transcription-factor regulated networks.These networks include a large number of components. The evolutionof these networks, which includes both TFs and their components,provides a snapshot of how complex organisms emerged and a basisfor the study of evolutionary developmental biology.

Acknowledgements

Not applicable.

Funding

DV would like to acknowledge funding from: i)Microsoft Azure for Genomics Research Grant (CRM:0740983); ii)FrailSafe Project (H2020-PHC-21-2015-690140) ‘Sensing andpredictive treatment of frailty and associated co-morbidities usingadvanced personalized models and advanced interventions’, co-fundedby the European Commission under the Horizon 2020 research andinnovation program; iii) Amazon Web Services Cloud for GenomicsResearch Grant (309211522729); iv) AdjustEBOVGP-Dx(RIA2018EF-2081): Biochemical Adjustments of native EBOVGlycoprotein in Patient Sample to Unmask target Epitopes for RapidDiagnostic Testing. A European and Developing Countries ClinicalTrials Partnership (EDCTP2) under the Horizon 2020 ‘Research andInnovation Actions’ DESCA. EE would like to acknowledge funding bythe project ‘INSPIRED-The National Research Infrastructures onIntegrated Structural Biology, Drug Screening Efforts and DrugTarget Functional Characterization’ (Grant MIS 5002550) and by theproject: ‘OPENSCREEN-GR An Open-Access Research Infrastructure ofChemical Biology and Target-Based Screening Technologies for Humanand Animal Health, Agriculture and the Environment’ (Grant MIS5002691), which are implemented under the Action ‘Reinforcement ofthe Research and Innovation Infrastructure’, funded by theOperational Programme ‘Competitiveness, Entrepreneurship andInnovation’ (NSRF 2014-2020) and co-financed by Greece and theEuropean Union (European Regional Development Fund).

Availability of data and materials

Not applicable.

Authors' contributions

TM, AE, FB, DV, GPC, EE have all equally contributedto the writing, drafting, revising, editing, reviewing, and theconception and design of the study. All authors have read andapproved the final manuscript.

Ethics approval and consent toparticipate

Not applicable.

Patient consent for publication

Not applicable.

Competing interests

The authors declare that they have no competinginterests.

References