Introduction
Gene regulation is a process of a controlled gene to be expressed into protein. The gene regulation in every organism is different on the specific and involved component in the process (Wong, 2016). Different complexity of structure between prokaryotes and eukaryotes affects the process of gene regulation. Bacteria is one of the prokaryotes which doesn’t have nuclei membrane, while human belongs to eukaryotes which has it. Because of that, bacteria could do transcription and translation at the same time (simultaneously), no inhuman (Miravet-Verde et al., 2017; Woldringh, 2002). The regulation of gene expression in bacteria composed of a multiply gene that controlled one promoter in the operon system called polycistronic (e.g. lac operon) (Silverstone & Magasanik, 1972), while the human is monocistronic which only has one gene controlled of one promoter. The structure of DNA itself in bacteria doesn’t require to be compacted by histone, while humans need it because of the long base pair of DNA that it must be contained inside the nucleus (Griswold, 2008). Thus, chromatin could control the gene expression to be able or not, with adding the acetyl or methyl on specific histone that it will affect different effect on gene expression (Martinez-Pastor et al., 2013). Therefore, the mechanism of gene regulation in the bacteria might be very simple than humans. However, some similarities and contrasts against these two gene systems might occur.
Transcription and regulation
The process to change the nucleotide DNA into RNA is called transcription. The transcription process in bacteria and humans is similar which is composed of three steps, initiation, elongation and termination. However, the complication of the process of each step is different because it depends on the component of protein available in the cell. Basically, most of the default of human gene is off, so the gene regulation is about to switch on the gene expression (positive regulation) by using activator (Figure 1), otherwise, bacteria gene is on and need to be switch off (negative regulation) by using repressor (Figure 2) (Hartl, 2018). However, both regulations also occur in both systems.
Regulation of transcription process in bacteria needs two types of DNA-protein interactions are promoter-RNA polymerase and operator-activators or repressor (Griffiths et al., 1999). If the RNA bind with the promoter with DNA site, it will begin the transcription process, however, it is controlled by the activator and repressor. If the activator-effector (protein at the allosteric site) bind to the DNA site will stimulate the transcription, otherwise, repressor protein-effector will bind to the operator then inhibit the transcription (Griffiths et al., 1999). There is an experiment according to Hobley et al. (2017), through the transcription process of the biofilm matrix exopolysaccharide in TasA operon, it needs a protein called spermidine to activate through regulator sIrR. In humans, the proteins involved in transcription are similar to bacteria. Promoter, activator, and repressor exist in human, also of repressor action may compete with an activator to the sequences in resulting of blocked or the repressor-active repression domain bind with transcription factor to inhibit the transcription. however many genes in mammalian cell especially human are controlled by regulatory sequences which located far away from transcription site called enhancer (Cooper, 2000). This sequence stimulates the transcription with no affecting the orientation nor distance (Figure 3). It also binds with protein to regulate the RNA polymerase and cause DNA looping (Figure 4) (Cooper, 2000).
All eukaryotic cell’s DNA is bound with histones, while no in bacteria. The binding forms chromatin, while the structural unit is called a nucleosome. This chromatin structure may affect the transcription process. In case, histone acetylation causes actively transcribed chromatin and may lose the binding of histones to DNA or affect interactions with another protein, nucleosome remodeling factor may provide the binding of transcription factor to the chromatin by changing the position of nucleosomes on the DNA, and DNA methylation may inhibit the transcription factor via protein action by modifying 5-carbon position of cytosine residue in DNA with methyl group (Cooper, 2000). Evidence of this epigenetic may affect the regulation of transcription according to Mamrut et al. (2013) on oxytocin hormone gene expression. The experiment used reporter gene assay to know the response of methylation of specific sites in the gene promoter. The results support evidently to inhibit the transcription and expression of the mouse oxytocin receptor gene (Mamrut et al., 2013).
(Hartl, 2018)
Figure 1. Positive regulation of transcription
(Hartl, 2018)
Figure 2. Negative regulation of transcription
(Cooper, 2000)
Figure 3. Enhancer action in human
(Cooper, 2000)
Figure 4. Interaction of enhancer and transcription factor in human
Initiation
The initiation process needs a promoter to initiate the running of the transcription or not. The promoter is a core region in the upstream of the genes or open reading frame (ORF). In bacteria, the promoter region recognizes a protein sigma factor as a protein to maneuver the RNA Polymerase enzyme to attach a specific sequence of the DNA. It has a lot different of sigma factor which has various function. According to Mauri (2014), there is another alternative sigma factor (σAl) which has the same function as the sigma factor (σ70) as housekeeping, these two proteins could bind with core RNA polymerase to form holoenzyme capable of unwinding the DNA double helix. In humans, it is more complex and uses more factors interaction. Generally, there are two kinds of a factor in human, transcription factor (TF) and sequence-binding with regulatory protein (Lambert et al., 2018). The factor will bind to the enhancer sequence which could connect with the promoter to stimulate the transcription process related to the gene. One of the examples of TF is POUF1 which could maintain the pluripotent of embryonic cells in the mouse (Boheler, 2009).
Bacteria have only single RNA Polymerase to generate different RNA (mRNA, tRNA, rRNA), while a human has different types of synthesis (Griffiths et al., 2000). The RNA Polymerase would bind with the core promoter region, one of them which has repeated T and A base pairs called TATA box. Both bacteria and human has the TATA box, however the element of the promoter region in human much more variation, including GC box and CCAAT box. TATA box is in 30 base pairs from the start site, and other boxes are found approximately in 100 and 200 base pairs from the start site (Figure 5) (Griffiths et al., 2000).
(Griffiths et al., 2000)
Figure 5. Promoter region in eukaryotes
Elongation
The elongation process occurs when the RNA polymerase has bound to the promoter. This process is similar between bacteria and humans, but in humans, the holoenzyme which plays a role in the synthesis of the sequence is RNA polymerase II (Griffiths et al., 2000). Some base-pair still exist like A, G, and C, and the change of T to U. The process will keep running until the termination signal occurred.
Termination
The termination process in bacteria is categorized by two types based on the associated protein, rho-independent and rho-dependent (Ciampi, 2006). In a single strand, the GC series will bind each other thus form stem-loop like. Because of that, the RNA polymerase will disassociate before U sequences. on the other mechanism, Rho-protein will bind with RNA which is not attached with ribosomes, thus, the single-strand will be packed up inside the rho protein, and caused it to break off with DNA template and RNA polymerase (Figure 6a) (Nadiras et al., 2018). This proposed by the experiment of Nadiras et al. (2018) by using the C>G template (rich C, and poor G) to induce the rho-protein signal, the result shows that Rho-protein generates a pattern on runoff transcripts compared to the control (Figure 6b). However, there are other mechanisms to propose termination which are called termination and antitermination. These kinds of termination are using terminator protein which could stop the elongation and induce the termination to lead to disassociate of RNA polymerase. Like E. coli trp operon, when the Trp levels are low, the antiterminator hairpin will form and Trp biosynthesis gene will be expressed, if the Trp levels are high the terminator hairpin will form and RNA polymerase will disassociate from the gene (Figure 7) (Santangelo & Artsimovitch, 2011). Otherwise, the process in eukaryotes especially human is still lack of understanding. The termination of different RNA in humans is transcribed by a different type of RNA polymerase. Basically, the termination protein will bind to DNA, so the RNA polymerase cannot synthesis the remaining sequence and will back off from the DNA template, unlike bacteria’s Rho-dependent mechanism in which the termination factor is binding with RNA. (Lodish et al., 2000).Pre-rRNA is transcribed of the RNA polymerase I and it needs a polymerase-specific termination factor binding to stop the elongation, while mRNA transcript is terminated of a protein complex which cleaves and polyadenylates it lead to suppressing termination (Lodish et al., 2000). Thus, RNA polymerase III will stop the elongation after polymerizing U residues (Lodish et al., 2000).
(Nadiras et al., 2018)
Figure 6. Termination process in bacteria, Rho-dependent mechanism (a) experiment by using C>G less DNA template generate cutting transcript, star symbol (b)
(Santangelo and Artsimovitch, 2011)
Figure 7. Termination and antitermination process
Post-transcriptional process
After the termination process, there is a different result of bacteria and human products. In bacteria, the end of the transcription process will generate final mRNA, however, inhuman is still generating pre-mRNA because the human’s DNA structure is more complex, it contains exon and intron sequence. The gene will express containing in exon sequence (Andreassi et al., 2018). So, the next process for humans is post-transcriptional modifications. In this process, the pre-mRNA will be modified of three parts, splicing intron, adding cap in the 5’ primer, and adding polyadenyl sequence in the 3’ prime (Poly-A) (Andreassi et al., 2018). Finally, the process will generate mRNA which could continue to translation. However, if the cell doesn’t need it, the mRNA will be degraded.
RNA Decaying
The mechanism of mRNA degradation between bacteria and humans is different. In general, bacteria’s mRNA is degraded by endonucleolytic cleavage, while the human's mRNA is decayed by deadenylation, decapping and exonucleolytic digestion (Belasco, 2010). Both bacteria and humans use short non-coding RNAs to regulate gene expression. Bacteria use sRNAs, while humans use microRNAs or small interfering RNAs. These non-coding RNAs can affect translation repression and lead to mRNA decay. Thereupon, there is an experiment that uses noncoding RNAs (CRISPR-Cas) to degrade the mRNA target (Zhu et al., 2018).
Conclusion
The gene regulation between bacteria and humans has similarities and differences. The process of the gene to be expressed is similar, also, a post-transcription process in humans, however, the complexity and component involved in the process and regulation are different. The bacteria mechanism is quite simple rather than human. After the process of transcription (post-transcription in human) can continue to be translated in the translation process in ribosomes or decay it if no necessary.
References
Andreassi, C., Crerar, H., Riccio, A., 2018. Post-transcriptional Processing of mRNA in Neurons: The Vestiges of the RNA World Drive Transcriptome Diversity. Front. Mol. Neurosci. 11. https://doi.org/10.3389/fnmol.2018.00304
Belasco, J.G., 2010. All things must pass: contrasts and commonalities in eukaryotic and bacterial mRNA decay. Nature Reviews Molecular Cell Biology 11, 467–478. https://doi.org/10.1038/nrm2917
Boheler, K.R., 2009. Stem Cell Pluripotency: A Cellular Trait that Depends on Transcription Factors, Chromatin State and a Checkpoint Deficient Cell Cycle. J Cell Physiol 221, 10–17. https://doi.org/10.1002/jcp.21866
Ciampi, M.S., 2006. Rho-dependent terminators and transcription termination. Microbiology 152, 2515–2528. https://doi.org/10.1099/mic.0.28982-0
Cooper, G.M., 2000. The Cell: A Molecular Approach. Sinauer Associates, Sunderland.
Griffiths, A.J., Gelbart, W.M., Miller, J.H., Lewontin, R.C., 1999. Modern Genetic Analysis. W. H. Freeman, New York.
Griffiths, A.J., Miller, J.H., Suzuki, D.T., Lewontin, R.C., Gelbart, W.M., 2000. An Introduction to Genetic Analysis. An Introduction to Genetic Analysis. 7th edition.
Griswold, A., 2008. Genome packaging in prokaryotes: the circular chromosome of E. coli. Nature Education 1,57.
Hartl, D.L., 2018. Essential Genetics and Genomics. Jones & Bartlett Learning.
Hobley, L., Li, B., Wood, J.L., Kim, S.H., Naidoo, J., Ferreira, A.S., Khomutov, M., Khomutov, A., Stanley-Wall, N.R., Michael, A.J., 2017. Spermidine promotes Bacillus subtilis biofilm formation by activating expression of the matrix regulator slrR. J. Biol. Chem. 292, 12041–12053. https://doi.org/10.1074/jbc.M117.789644
Lambert, S.A., Jolma, A., Campitelli, L.F., Das, P.K., Yin, Y., Albu, M., Chen, X., Taipale, J., Hughes, T.R., Weirauch, M.T., 2018. The Human Transcription Factors. Cell 172, 650–665. https://doi.org/10.1016/j.cell.2018.01.029
Lodish, H., Berk, A., Zipursky, S.L., Matsudaira, P., Baltimore, D., Darnell, J., 2000. Molecular Cell Biology: transcription termination. Molecular Cell Biology. 4th edition.
Mamrut, S., Harony, H., Sood, R., Shahar-Gold, H., Gainer, H., Shi, Y.-J., Barki-Harrington, L., Wagner, S., 2013. DNA Methylation of Specific CpG Sites in the Promoter Region Regulates the Transcription of the Mouse Oxytocin Receptor. PLOS ONE 8, e56869. https://doi.org/10.1371/journal.pone.0056869
Mauri, M., Klumpp, S., 2014. A Model for Sigma Factor Competition in Bacterial Cells. PLOS Computational Biology 10, e1003845. https://doi.org/10.1371/journal.pcbi.1003845
Martinez-Pastor, B., Cosentino, C., Mostoslavsky, R., 2013. A tale of metabolites: the crosstalk between chromatin and energy metabolism. Cancer Discov 3, 497–501. https://doi.org/10.1158/2159-8290.CD-13-0059
Miravet-Verde, S., Lloréns-Rico, V., Serrano, L., 2017. Alternative transcriptional regulation in genome-reduced bacteria. Current Opinion in Microbiology, Antimicrobials * Bacterial Systems Biology 39, 89–95. https://doi.org/10.1016/j.mib.2017.10.022
Nadiras, C., Eveno, E., Schwartz, A., Figueroa-Bossi, N., Boudvillain, M., 2018. A multivariate prediction model for Rho-dependent termination of transcription. Nucleic Acids Res 46, 8245–8260. https://doi.org/10.1093/nar/gky563
Silverstone, A.E., Magasanik, B., 1972. Polycistronic Effects of Catabolite Repression on the lac Operon. J Bacteriol 112, 1184–1192.
Santangelo, T.J., Artsimovitch, I., 2011. Termination and antitermination: RNA polymerase runs a stop sign. Nature Reviews Microbiology 9, 319–329. https://doi.org/10.1038/nrmicro2560
Woldringh, C.L., 2002. The role of co-transcriptional translation and protein translocation (transertion) in bacterial chromosome segregation. Mol. Microbiol. 45, 17–29. https://doi.org/10.1046/j.1365-2958.2002.02993.x
Wong, K.-C., 2016. Computational Biology and Bioinformatics: Gene Regulation. CRC Press.
Zhu, Y., Klompe, S.E., Vlot, M., van der Oost, J., Staals, R.H.J., 2018. Shooting the messenger: RNA-targetting CRISPR-Cas systems. Biosci Rep 38. https://doi.org/10.1042/BSR20170788
0 Comments