Self-Organization and Information Processing: From Basic Enzymatic Activities to Complex Adaptive Cellular Behavior

Systemic cellular migration: The forces driving the directed locomotion movement of cells

Directional motility is an essential property of cells. Despite its enormous relevance in many fundamental physiological and pathological processes, how cells control their locomotion movements remains an unresolved question. Here, we have addressed the systemic processes driving the directed locomotion of cells. Specifically, we have performed an exhaustive study analyzing the trajectories of 700 individual cells belonging to three different species (Amoeba proteus, Metamoeba leningradensis, and Amoeba borokensis) in four different scenarios: in absence of stimuli, under an electric field (galvanotaxis), in a chemotactic gradient (chemotaxis), and under simultaneous galvanotactic and chemotactic stimuli. All movements were analyzed using advanced quantitative tools. The results show that the trajectories are mainly characterized by coherent integrative responses that operate at the global cellular scale. These systemic migratory movements depend on the cooperative nonlinear interaction of most, if not all, molecular components of cells.

Purification and biochemical characterization of novel α-amylase and cellulase from Bacillus sp. PM06

Bacillus sp. PM06, previously isolated from sugarcane waste pressmud, could produce dual enzymes α-amylase and cellulase. The isolate's crude enzymes were purified homogeneously using ammonium sulfate precipitation followed by High Quaternary amine anion exchange chromatography. Purified enzymes revealed the molecular weights of α-amylase and cellulase as 55 and 52 kDa, with a purification fold of 15.4 and 11.5, respectively. The specific activity of purified α-amylase and cellulase were 740.7 and 555.6 U/mg, respectively. It demonstrated a wide range of activity from pH 5.0 to 8.5, with an optimum pH of 5.5 and 6.4 for α-amylase and cellulase. The optimum temperature was 50 °C for α-amylase and 60 °C for cellulase. The kinetic parameters of purified α-amylase were 741.5 ± 3.75 µmol/min/mg, 1.154 ± 0.1 mM, and 589 ± 3.5/(s mM), using starch as a substrate. Whereas cellulase showed 556.3 ± 1.3 µmol/min/mg, 1.78 ± 0.1 mM, and 270.9 ± 3.8/(s mM) of Vmax, Km, Kcat/Km, respectively, using carboxymethyl cellulose (CMC) as substrate. Among the various substrates tested, α-amylase had a higher specificity for amylose and CMC for cellulase. Different inhibitors and activators were also examined. Ca2+ Mg2+, Co2+, and Mn2+ boosted α-amylase and cellulase activities. Cu2+ and Ni2+ both inhibited the enzyme activities. Enzymatic saccharification of wheat bran yielded 253.61 ± 1.7 and 147.5 ± 1.0 mg/g of reducing sugar within 12 and 24 h of incubation when treated with purified α-amylase and cellulase. A more significant amount of 397.7 ± 1.9 mg/g reducing sugars was released from wheat bran due to the synergetic effect of two enzymes. According to scanning electron micrograph analysis, wheat bran was effectively broken down by both enzymes.

The origin of genetic and metabolic systems: Evolutionary structuralinsights

DNA is derived from reverse transcription and its origin is related to reverse transcriptase, DNA polymerase and integrase. The gene structure originated from the evolution of the first RNA polymerase. Thus, an explanation of the origin of the genetic system must also explain the evolution of these enzymes. This paper proposes a polymer structure model, termed the stable complex evolution model, which explains the evolution of enzymes and functional molecules. Enzymes evolved their functions by forming locally tightly packed complexes with specific substrates. A metabolic reaction can therefore be considered to be the result of adaptive evolution in this way when a certain essential molecule is lacking in a cell. The evolution of the primitive genetic and metabolic systems was thus coordinated and synchronized. According to the stable complex model, almost all functional molecules establish binding affinity and specific recognition through complementary interactions, and functional molecules therefore have the nature of being auto-reactive. This is thermodynamically favorable and leads to functional duplication and self-organization. Therefore, it can be speculated that biological systems have a certain tendency to maintain functional stability or are influenced by an inherent selective power. The evolution of dormant bacteria may support this hypothesis, and inherent selectivity can be unified with natural selection at the molecular level.

The Binding of Different Substrate Molecules at the Docking Site and the Active Site of γ-Secretase Can Trigger Toxic Events in Sporadic and Familial Alzheimer's Disease

Pathogenic changes in γ-secretase activity, along with its response to different drugs, can be affected by changes in the saturation of γ-secretase with its substrate. We analyze the saturation of γ-secretase with its substrate using multiscale molecular dynamics studies. We found that an increase in the saturation of γ-secretase with its substrate could result in the parallel binding of different substrate molecules at the docking site and the active site. The C-terminal domain of the substrate bound at the docking site can interact with the most dynamic presenilin sites at the cytosolic end of the active site tunnel. Such interactions can inhibit the ongoing catalytic activity and increase the production of the longer, more hydrophobic, and more toxic Aβ proteins. Similar disruptions in dynamic presenilin structures can be observed with different drugs and disease-causing mutations. Both, C99-βCTF-APP substrate and its different Aβ products, can support the toxic aggregation. The aggregation depends on the substrate N-terminal domain. Thus, the C99-βCTF-APP substrate and β-secretase path can be more toxic than the C83-αCTF-APP substrate and α-secretase path. Nicastrin can control the toxic aggregation in the closed conformation. The binding of the C99-βCTF-APP substrate to γ-secretase can be controlled by substrate channeling between the nicastrin and β-secretase. We conclude that the presented two-substrate mechanism could explain the pathogenic changes in γ-secretase activity and Aβ metabolism in different sporadic and familial cases of Alzheimer's disease. Future drug-development efforts should target different cellular mechanisms that regulate the optimal balance between γ-secretase activity and amyloid metabolism.

Monofunctional Heme-Catalases

The review focuses on four issues that are critical for the understanding of monofunctional catalases. How hydrogen peroxide (H2O2) reaches the active site and outcompetes water molecules to be able to function at a very high rate is one of the issues examined. Part of the answer is a gate valve system that is instrumental to drive out solvent molecules from the final section of the main channel. A second issue relates to how the enzyme deals with an unproductive reactive compound I (Cpd I) intermediate. Peroxidatic two and one electron donors and the transfer of electrons to the active site from NADPH and other compounds are reviewed. The new ascribed catalase reactions are revised, indicating possible measurement pitfalls. A third issue concerns the heme b to heme d oxidation, why this reaction occurs only in some large-size subunit catalases (LSCs), and the possible role of singlet oxygen in this and other modifications. The formation of a covalent bond between the proximal tyrosine with the vicinal residue is analyzed. The last issue refers to the origin and function of the additional C-terminal domain (TD) of LSCs. The TD has a molecular chaperone activity that is traced to a gene fusion between a Hsp31-type chaperone and a small-size subunit catalase (SSC).

Cellular sentience as the primary source of biological order and evolution

All life is cellular, starting some 4 billion years ago with the emergence of the first cells. In order to survive their early evolution in the face of an extremely challenging environment, the very first cells invented cellular sentience and cognition, allowing them to make relevant decisions to survive through creative adaptations in a continuously running evolutionary narrative. We propose that the success of cellular life has crucially depended on a biological version of Maxwell's demons which permits the extraction of relevant sensory information and energy from the cellular environment, allowing cells to sustain anti-entropic actions. These sensor-effector actions allowed for the creative construction of biological order in the form of diverse organic macromolecules, including crucial polymers such as DNA, RNA, and cytoskeleton. Ordered biopolymers store analogue (structures as templates) and digital (nucleotide sequences of DNA and RNA) information that functioned as a form memory to support the development of organisms and their evolution. Crucially, all cells are formed by the division of previous cells, and their plasma membranes are physically and informationally continuous across evolution since the beginning of cellular life. It is argued that life is supported through life-specific principles which support cellular sentience, distinguishing life from non-life. Biological order, together with cellular cognition and sentience, allow the creative evolution of all living organisms as the authentic authors of evolutionary novelty.

Correspondence insights into the role of genes in cell functionality. Comments on "The gene: An appraisal" by K. Baverstock

One of the most important goals of the post-genomic era is to understand the different sources of molecular information that regulate the functional and structural architecture of cells. In this regard, Prof. K. Baverstock underscores in his recent article "The gene: An appraisal" (Baverstock, 2021) that genes are not the leading elements in cellular functionality, inheritance and evolution. As a consequence, the theory of evolution based on the Neo-Darwinian synthesis, is inadequate for today's scientific evidence. Conversely, the author contends that life processes viewed on the basis of thermodynamics, complex system dynamics and self-organization provide a new framework for the foundations of Biology. I consider it necessary to comment on some essential aspects of this relevant work, and here I present a short overview of the main non-genetic sources of biomolecular order and complexity that underline the molecular dynamics and functionality of cells. These sources generate different processes of complexity, which encompasses from the most elementary levels of molecular activity to the emergence of systemic behaviors, and the information necessary to sustain them is not contained in the genome.

Associative Conditioning Is a Robust Systemic Behavior in Unicellular Organisms: An Interspecies Comparison

The capacity to learn new efficient systemic behavior is a fundamental issue of contemporary biology. We have recently observed, in a preliminary analysis, the emergence of conditioned behavior in some individual amoebae cells. In these experiments, cells were able to acquire new migratory patterns and remember them for long periods of their cellular cycle, forgetting them later on. Here, following a similar conceptual framework of Pavlov's experiments, we have exhaustively studied the migration trajectories of more than 2000 individual cells belonging to three different species: Amoeba proteus, Metamoeba leningradensis, and Amoeba borokensis. Fundamentally, we have analyzed several relevant properties of conditioned cells, such as the intensity of the responses, the directionality persistence, the total distance traveled, the directionality ratio, the average speed, and the persistence times. We have observed that cells belonging to these three species can modify the systemic response to a specific stimulus by associative conditioning. Our main analysis shows that such new behavior is very robust and presents a similar structure of migration patterns in the three species, which was characterized by the presence of conditioning for long periods, remarkable straightness in their trajectories and strong directional persistence. Our experimental and quantitative results, compared with other studies on complex cellular responses in bacteria, protozoa, fungus-like organisms and metazoans that we discus here, allow us to conclude that cellular associative conditioning might be a widespread characteristic of unicellular organisms. This new systemic behavior could be essential to understand some key principles involved in increasing the cellular adaptive fitness to microenvironments.