May the Odds Be Ever in Your Favor: Non-deterministic Mechanisms Diversifying Cell Surface Molecule Expression

Exploring the Evolution-Coupling Hypothesis: Do Enzymes' Performance Gains Correlate with Increased Dissipation?

The research literature presents divergent opinions regarding the role of dissipation in living systems, with views ranging from it being useless to it being essential for driving life. The implications of universal thermodynamic evolution are often overlooked or considered controversial. A higher rate of entropy production indicates faster thermodynamic evolution. We calculated enzyme-associated dissipation under steady-state conditions using minimalistic models of enzyme kinetics when all microscopic rate constants are known. We found that dissipation is roughly proportional to the turnover number, and a log-log power-law relationship exists between dissipation and the catalytic efficiency of enzymes. "Perfect" specialized enzymes exhibit the highest dissipation levels and represent the pinnacle of biological evolution. The examples that we analyzed suggested two key points: (a) more evolved enzymes excel in free-energy dissipation, and (b) the proposed evolutionary trajectory from generalist to specialized enzymes should involve increased dissipation for the latter. Introducing stochastic noise in the kinetics of individual enzymes may lead to optimal performance parameters that exceed the observed values. Our findings indicate that biological evolution has opened new channels for dissipation through specialized enzymes. We also discuss the implications of our results concerning scaling laws and the seamless coupling between thermodynamic and biological evolution in living systems immersed in out-of-equilibrium environments.

DNA damage drives antigen diversification through mosaic Variant Surface Glycoprotein (VSG) formation in Trypanosoma brucei

Antigenic variation, using large genomic repertoires of antigen-encoding genes, allows pathogens to evade host antibody. Many pathogens, including the African trypanosome Trypanosoma brucei, extend their antigenic repertoire through genomic diversification. While evidence suggests that T. brucei depends on the generation of new variant surface glycoprotein (VSG) genes to maintain a chronic infection, a lack of experimentally tractable tools for studying this process has obscured its underlying mechanisms. Here, we present a highly sensitive targeted sequencing approach for measuring VSG diversification. Using this method, we demonstrate that a Cas9-induced DNA double-strand break within the VSG coding sequence can induce VSG recombination with patterns identical to those observed during infection. These newly generated VSGs are antigenically distinct from parental clones and thus capable of facilitating immune evasion. Together, these results provide insight into the mechanisms of VSG diversification and an experimental framework for studying the evolution of antigen repertoires in pathogenic microbes.

Spatial constraints and cell surface molecule depletion structure a randomly connected learning circuit

The brain can represent almost limitless objects to "categorize an unlabeled world" (Edelman, 1989). This feat is supported by expansion layer circuit architectures, in which neurons carrying information about discrete sensory channels make combinatorial connections onto much larger postsynaptic populations. Combinatorial connections in expansion layers are modeled as randomized sets. The extent to which randomized wiring exists in vivo is debated, and how combinatorial connectivity patterns are generated during development is not understood. Non-deterministic wiring algorithms could program such connectivity using minimal genomic information. Here, we investigate anatomic and transcriptional patterns and perturb partner availability to ask how Kenyon cells, the expansion layer neurons of the insect mushroom body, obtain combinatorial input from olfactory projection neurons. Olfactory projection neurons form their presynaptic outputs in an orderly, predictable, and biased fashion. We find that Kenyon cells accept spatially co-located but molecularly heterogeneous inputs from this orderly map, and ask how Kenyon cell surface molecule expression impacts partner choice. Cell surface immunoglobulins are broadly depleted in Kenyon cells, and we propose that this allows them to form connections with molecularly heterogeneous partners. This model can explain how developmentally identical neurons acquire diverse wiring identities.

Theoretical Improvements in Enzyme Efficiency Associated with Noisy Rate Constants and Increased Dissipation

Previous studies have revealed the extraordinarily large catalytic efficiency of some enzymes. High catalytic proficiency is an essential accomplishment of biological evolution. Natural selection led to the increased turnover number, kcat, and enzyme efficiency, kcat/KM, of uni-uni enzymes, which convert a single substrate into a single product. We added or multiplied random noise with chosen rate constants to explore the correlation between dissipation and catalytic efficiency for ten enzymes: beta-galactosidase, glucose isomerase, β-lactamases from three bacterial strains, ketosteroid isomerase, triosephosphate isomerase, and carbonic anhydrase I, II, and T200H. Our results highlight the role of biological evolution in accelerating thermodynamic evolution. The catalytic performance of these enzymes is proportional to overall entropy production-the main parameter from irreversible thermodynamics. That parameter is also proportional to the evolutionary distance of β-lactamases PC1, RTEM, and Lac-1 when natural or artificial evolution produces the optimal or maximal possible catalytic efficiency. De novo enzyme design and attempts to speed up the rate-limiting catalytic steps may profit from the described connection between kinetics and thermodynamics.

An allele-selective inter-chromosomal protein bridge supports monogenic antigen expression in the African trypanosome

UPF1-like helicases play roles in telomeric heterochromatin formation and X-chromosome inactivation, and also in monogenic variant surface glycoprotein (VSG) expression via VSG exclusion-factor-2 (VEX2), a UPF1-related protein in the African trypanosome. We show that VEX2 associates with chromatin specifically at the single active VSG expression site on chromosome 6, forming an allele-selective connection, via VEX1, to the trans-splicing locus on chromosome 9, physically bridging two chromosomes and the VSG transcription and splicing compartments. We further show that the VEX-complex is multimeric and self-regulates turnover to tightly control its abundance. Using single cell transcriptomics following VEX2-depletion, we observed simultaneous derepression of many other telomeric VSGs and multi-allelic VSG expression in individual cells. Thus, an allele-selective, inter-chromosomal, and self-limiting VEX1-2 bridge supports monogenic VSG expression and multi-allelic VSG exclusion.

Emergence and influence of sequence bias in evolutionarily malleable, mammalian tandem arrays

BACKGROUND

The radiation of mammals at the extinction of the dinosaurs produced a plethora of new forms-as diverse as bats, dolphins, and elephants-in only 10-20 million years. Behind the scenes, adaptation to new niches is accompanied by extensive innovation in large families of genes that allow animals to contact the environment, including chemosensors, xenobiotic enzymes, and immune and barrier proteins. Genes in these "outward-looking" families are allelically diverse among humans and exhibit tissue-specific and sometimes stochastic expression.

RESULTS

Here, we show that these tandem arrays of outward-looking genes occupy AT-biased isochores and comprise the "tissue-specific" gene class that lack CpG islands in their promoters. Models of mammalian genome evolution have not incorporated the sharply different functions and transcriptional patterns of genes in AT- versus GC-biased regions. To examine the relationship between gene family expansion, sequence content, and allelic diversity, we use population genetic data and comparative analysis. First, we find that AT bias can emerge during evolutionary expansion of gene families in cis. Second, human genes in AT-biased isochores or with GC-poor promoters experience relatively low rates of de novo point mutation today but are enriched for non-synonymous variants. Finally, we find that isochores containing gene clusters exhibit low rates of recombination.

CONCLUSIONS

Our analyses suggest that tolerance of non-synonymous variation and low recombination are two forces that have produced the depletion of GC bases in outward-facing gene arrays. In turn, high AT content exerts a profound effect on their chromatin organization and transcriptional regulation.

The role of LncRNA LBX2-AS1 in cancers: functions, mechanisms and potential clinical utility

Increasingly advanced biology technique has revealed that long non-coding RNAs (lncRNA) as critical factors that exert significant regulatory effects on biological functions by modulating gene transcription, epigenetic modifications and protein translation. A newly emerging lncRNA, ladybird homeobox 2 (LBX2)-antisense RNA 1 (LBX2-AS1), was found to be highly expressed in various tumors. Moreover, it is functionally linked to the regulation of essential tumor-related biological processes, such as cell proliferation and apoptosis, through interactions with multiple signaling molecules/pathways. The important roles played by LBX2-AS1 in cancer initiation and progression suggest that this lncRNA has enormous clinical potential for use as a novel biomarker or therapeutic target. In this article, we retrospectively review the latest advances in research exploring the roles of the lncRNA LBX2-AS1 in oncology field, highlighting its involvement in a comprehensive network of molecular mechanisms underlying diverse cancers and examining its potential applications in clinical practice.

Olfactory dysfunction in patients with multiple sclerosis; A systematic review and meta-analysis

Background

The importance and prevalence of olfactory dysfunction is recently gaining attention in patients with multiple sclerosis (MS) as a result of their chronic inflammatory disease, yet different prevalence rates are reported for it. Therefore, we have designed this systematic review to estimate the pooled prevalence of olfactory dysfunction in patients with MS. To our knowledge, this is the first systematic review and meta-analysis on the prevalence of olfactory dysfunction in MS patients.

Methods

We searched PubMed, Scopus, EMBASE, Web of Science, ProQuest, and gray literature including references from the identified studies, review studies, and conference abstracts which were published up to January 2021. Articles that were relevant to our topic and could provide information regarding the prevalence of olfactory dysfunction, or the scores of smell threshold, discrimination, or identification (TDI) among MS patients and healthy individuals were included. The pooled prevalence was calculated using a random-effects model and a funnel plot and Egger’s regression test were used to see publication bias.

Results

The literature search found 1630 articles. After eliminating duplicates, 897 articles remained. Two conference abstracts were included for final analysis. A total of 1099 MS cases and 299 MS patients with olfactory dysfunction were included in the analysis. The pooled prevalence of olfactory dysfunction in the included studies was 27.2%. Also, the overall TDI score in MS patients was lower than that in the control group, and the level of Threshold, Discrimination, and Identification per se were lower in MS compared with control respectively.

Conclusion

The results of this systematic review show that the prevalence of olfactory dysfunction in MS patients is high and more attention needs to be drawn to this aspect of MS.