Organization of the genome: by evolution, or design?
https://reasonandscience.catsboard.com/t3092-organization-of-the-genome-by-evolution-or-design
Multiple protein subunits come together to form protein complexes that play critical functional roles in a cell. The arrangement of genes is a key factor that modulates the variation of protein complexes. Proteins are synthesized in specific orders to assemble large protein complexes, such as microtubule, proteasome, ribosomes, and cellulosome. These protein complexes are assembled both inside and outside cells through the coordination of gene expression, protein transport, and binding processes. Protein complexes can compose of different cofactors, post-translational modifications, and protein membership. Genetic circuits, physical transport, and binding kinetic rates all modulate the distribution of complexoform. The interplay between the circuit architecture and the genetic and physical rate kinetics together determine the protein assembly structure. 3
Operon Gene Order Is Optimized for Ordered Protein Complex Assembly 2 February 2016
There is a remarkable correspondence between gene order and protein assembly order. The gene order has a significant effect and helps in the protein subunit assembly. Operon gene order is optimized to match the order in which protein subunits assemble. Many operons contain genes encoding different subunits of the same protein complex. There is a significant benefit from tightly coordinating gene expression and protein assembly.2
My comment: How did that state of affairs come to be without foreknowledge of how protein multisubunit assembly has to be performed and involving ordering principles which are known to come from a mind? Subunits confer no function unless their use is known in the heterogeneous organization ( proteins composed of different subunits), formed from multiple distinct protein subunits, and completed into the much larger system. How was this corresponding order achieved? Where gene sequences stochastically formed by mutations, and trial and error explored assembly space possibilities until a particular sequential functional order and finally functional heteromeric subunit combination of protein complexes was "discovered"? If that were so, the cell would have been producing a considerable number of nonfunctional proteins assembled in the wrong way. In that process, deleterious genetic mutations would probably be eliminated by selection, long before a new protein assembly sequence would be explored and become functional.
Furthermore, the timing and location of translation have also to be co-ordinated and are important for maximizing the efficiency of stochastic protein complex assembly.
Stochastic ordering of complexoform protein assembly by genetic circuits3 June 29, 2020
The different molecular forms of a protein complex have come to be called “complex isoform” or “complexoform”. Genes arranged in a single operon, a cascade, or as two operons all give rise to the different protein composition of complexoform because of timing differences in protein-synthesis order. With biologically relevant rates, we find that the genetic circuitry controls the average final complexoform assembly and the variation in the assembly structure. Our results highlight the importance of both the genetic circuit architecture and kinetics in determining the distribution of a complexoform.
Spatial Genome Organization: From Development to Disease 21 March 2019
Chromosomes are organized in discrete territories within the nucleus. Even prokaryotic chromosome is organized into TADs resembling those in higher organisms. Higher-order associations of TADs form A and B compartments which are typically enriched in transcriptionally active and inactive chromatin, respectively. The first level of higher-order chromosome organization is the presence of megabase-sized blocks, called Topologically Associated Domains (TADs). A certain degree of order is achieved in the system merely through entropic forces and stabilized by genome-wide transcriptional events. Architectural proteins like CTCF and cohesin confer stability to this order and might facilitate genome reorganization, aiding in accurate Spatio-temporal gene-expression during development. 1
1. https://www.frontiersin.org/articles/10.3389/fcell.2019.00018/full
2. https://www.cell.com/cell-reports/pdf/S2211-1247(15)01541-7.pdf
3. https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007997
https://reasonandscience.catsboard.com/t3092-organization-of-the-genome-by-evolution-or-design
Multiple protein subunits come together to form protein complexes that play critical functional roles in a cell. The arrangement of genes is a key factor that modulates the variation of protein complexes. Proteins are synthesized in specific orders to assemble large protein complexes, such as microtubule, proteasome, ribosomes, and cellulosome. These protein complexes are assembled both inside and outside cells through the coordination of gene expression, protein transport, and binding processes. Protein complexes can compose of different cofactors, post-translational modifications, and protein membership. Genetic circuits, physical transport, and binding kinetic rates all modulate the distribution of complexoform. The interplay between the circuit architecture and the genetic and physical rate kinetics together determine the protein assembly structure. 3
Operon Gene Order Is Optimized for Ordered Protein Complex Assembly 2 February 2016
There is a remarkable correspondence between gene order and protein assembly order. The gene order has a significant effect and helps in the protein subunit assembly. Operon gene order is optimized to match the order in which protein subunits assemble. Many operons contain genes encoding different subunits of the same protein complex. There is a significant benefit from tightly coordinating gene expression and protein assembly.2
My comment: How did that state of affairs come to be without foreknowledge of how protein multisubunit assembly has to be performed and involving ordering principles which are known to come from a mind? Subunits confer no function unless their use is known in the heterogeneous organization ( proteins composed of different subunits), formed from multiple distinct protein subunits, and completed into the much larger system. How was this corresponding order achieved? Where gene sequences stochastically formed by mutations, and trial and error explored assembly space possibilities until a particular sequential functional order and finally functional heteromeric subunit combination of protein complexes was "discovered"? If that were so, the cell would have been producing a considerable number of nonfunctional proteins assembled in the wrong way. In that process, deleterious genetic mutations would probably be eliminated by selection, long before a new protein assembly sequence would be explored and become functional.
Furthermore, the timing and location of translation have also to be co-ordinated and are important for maximizing the efficiency of stochastic protein complex assembly.
Stochastic ordering of complexoform protein assembly by genetic circuits3 June 29, 2020
The different molecular forms of a protein complex have come to be called “complex isoform” or “complexoform”. Genes arranged in a single operon, a cascade, or as two operons all give rise to the different protein composition of complexoform because of timing differences in protein-synthesis order. With biologically relevant rates, we find that the genetic circuitry controls the average final complexoform assembly and the variation in the assembly structure. Our results highlight the importance of both the genetic circuit architecture and kinetics in determining the distribution of a complexoform.
Spatial Genome Organization: From Development to Disease 21 March 2019
Chromosomes are organized in discrete territories within the nucleus. Even prokaryotic chromosome is organized into TADs resembling those in higher organisms. Higher-order associations of TADs form A and B compartments which are typically enriched in transcriptionally active and inactive chromatin, respectively. The first level of higher-order chromosome organization is the presence of megabase-sized blocks, called Topologically Associated Domains (TADs). A certain degree of order is achieved in the system merely through entropic forces and stabilized by genome-wide transcriptional events. Architectural proteins like CTCF and cohesin confer stability to this order and might facilitate genome reorganization, aiding in accurate Spatio-temporal gene-expression during development. 1
1. https://www.frontiersin.org/articles/10.3389/fcell.2019.00018/full
2. https://www.cell.com/cell-reports/pdf/S2211-1247(15)01541-7.pdf
3. https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007997
