The dynamic nature of the K-Ras/calmodulin complex can be altered by oncogenic mutations

Microbial-induced calcium precipitation: Bibliometric analysis, reaction mechanisms, mineralization types, and perspectives

Microbial-induced calcium precipitation (MICP) refers to the formation of calcium precipitates induced by mineralization during microbial metabolism. MICP has been widely used as an ecologically sustainable method in environmental, geotechnical, and construction fields. This article reviews the removal mechanisms of MICP for different contaminants in the field of water treatment. The nucleation pathway is explained at both extracellular and intracellular levels, with a focus on evaluating the contribution of extracellular polymers to MICP. The types of mineralization and the regulatory role of enzyme genes in the MICP process are innovatively summarized. Based on this, the environmental significance of MICP is illustrated, and the application prospects of calcium precipitation products are discussed. The research hotspots and development trends of MICP are analyzed by bibliometric methods, and the challenges and future directions of MICP technology are identified. This review aims to provide a theoretical basis for further understanding of the MICP phenomenon in water treatment and the effective removal of multiple pollutants, which will help researchers to find the breakthroughs and innovations in the existing technologies, with a view to making significant progress in MICP technology.

Energetic and structural insights behind calcium induced conformational transition in calmodulin

Calmodulin (CaM) is a key signaling protein that triggers several cellular and physiological processes inside the cell. Upon binding with calcium ion, CaM undergoes large scale conformational transition from a closed state to an open state that facilitates its interaction with various target protein and regulates their activity. This work explores the origin of the energetic and structural variation of the wild type and mutated CaM and explores the molecular origin for the structural differences between them. We first calculated the sequential calcium binding energy to CaM using the PDLD/S-LRA/β approach. This study  shows a very good correlation with experimental calcium binding energies. Next we calculated the calcium binding energies to the wild type CaM and several mutated CaM systems which were reported experimentally. On the structural aspect, it has been reported experimentally that certain mutation (Q41L-K75I) in calcium bound CaM leads to complete conformational transition from an open to a closed state. By using equilibrium molecular dynamics simulation, free energy calculation and contact frequency map analysis, we have shown that the formation of a cluster of long-range hydrophobic contacts, initiated by the Q41L-K75I CaM variant is the driving force behind its closing motion. This study unravels the energetics and structural aspects behind calcium ion induced conformational changes in wild type CaM and its variant.

Cell phenotypes can be predicted from propensities of protein conformations

Proteins exist as dynamic conformational ensembles. Here we suggest that the propensities of the conformations can be predictors of cell function. The conformational states that the molecules preferentially visit can be viewed as phenotypic determinants, and their mutations work by altering the relative propensities, thus the cell phenotype. Our examples include (i) inactive state variants harboring cancer driver mutations that present active state-like conformational features, as in K-Ras4BG12V compared to other K-Ras4BG12X mutations; (ii) mutants of the same protein presenting vastly different phenotypic and clinical profiles: cancer and neurodevelopmental disorders; (iii) alterations in the occupancies of the conformational (sub)states influencing enzyme reactivity. Thus, protein conformational propensities can determine cell fate. They can also suggest the allosteric drugs efficiency.

Protein conformational ensembles in function: roles and mechanisms

The sequence-structure-function paradigm has dominated twentieth century molecular biology. The paradigm tacitly stipulated that for each sequence there exists a single, well-organized protein structure. Yet, to sustain cell life, function requires (i) that there be more than a single structure, (ii) that there be switching between the structures, and (iii) that the structures be incompletely organized. These fundamental tenets called for an updated sequence-conformational ensemble-function paradigm. The powerful energy landscape idea, which is the foundation of modernized molecular biology, imported the conformational ensemble framework from physics and chemistry. This framework embraces the recognition that proteins are dynamic and are always interconverting between conformational states with varying energies. The more stable the conformation the more populated it is. The changes in the populations of the states are required for cell life. As an example, in vivo, under physiological conditions, wild type kinases commonly populate their more stable "closed", inactive, conformations. However, there are minor populations of the "open", ligand-free states. Upon their stabilization, e.g., by high affinity interactions or mutations, their ensembles shift to occupy the active states. Here we discuss the role of conformational propensities in function. We provide multiple examples of diverse systems, including protein kinases, lipid kinases, and Ras GTPases, discuss diverse conformational mechanisms, and provide a broad outlook on protein ensembles in the cell. We propose that the number of molecules in the active state (inactive for repressors), determine protein function, and that the dynamic, relative conformational propensities, rather than the rigid structures, are the hallmark of cell life.

Microbially induced calcium precipitation driven by denitrification: Performance, metabolites, and molecular mechanisms

Microbially induced calcium precipitation (MICP) driven by denitrification has attracted extensive attention due to its application potential in nitrate removal from calcium-rich groundwater. However, little research has been conducted on this technique at the molecular level. Here, Pseudomonas WZ39 was used to explore the molecular mechanisms of nitrate-dependent MICP and the effects of Ca²⁺ on bacterial transcriptional regulation and metabolic response. The results exhibited that appropriate Ca²⁺ concentration (4.5 mM) can promote denitrification and the production of ATP, EPSs, and SMPs. Genome-wide analysis showed that the nitrate-dependent MICP was accomplished through heterotrophic denitrification and CO₂ capture. During this process, EPS biosynthesis and Ca²⁺ signaling regulation were involved in the nucleation template supply and Ca²⁺ homeostasis balance. Untargeted transcriptome- and metabolome-association analyses revealed that the addition of Ca²⁺ triggered the significant up-regulation in several key pathways, such as transmembrane transporter and channel activities, amino acid metabolism, fatty acid biosynthesis, and carbon metabolism, which played a momentous role in the mineral nucleation and energy provision. The detailed information provided novel insights for understanding the active control of bacteria on MICP, and has great significance for deepening the cognition of groundwater remediation using nitrate-dependent MICP technique.

K-Ras Binds Calmodulin-Related Centrin1 with Potential Implications for K-Ras Driven Cancer Cell Stemness

Recent data suggest that K-Ras4B (hereafter K-Ras) can drive cancer cell stemness via calmodulin (CaM)-dependent, non-canonical Wnt-signalling. Here we examined whether another Ca²⁺-binding protein, the CaM-related centrin1, binds to K-Ras and could mediate some K-Ras functions that were previously ascribed to CaM. While CaM and centrin1 appear to distinguish between peptides that were derived from their classical targets, they both bind to K-Ras in cells. Cellular BRET- and immunoprecipitation data suggest that CaM engages more with K-Ras than centrin1 and that the interaction with the C-terminal membrane anchor of K-Ras is sufficient for this. Surprisingly, binding of neither K-Ras nor its membrane anchor alone to CaM or centrin1 is sensitive to inhibition of prenylation. In support of an involvement of the G-domain of K-Ras in cellular complexes with these Ca²⁺-binding proteins, we find that oncogenic K-RasG12V displays increased engagement with both CaM and centrin1. This is abrogated by addition of the D38A effector-site mutation, suggesting that K-RasG12V is held together with CaM or centrin1 in complexes with effectors. When treated with CaM inhibitors, the BRET-interaction of K-RasG12V with centrin1 was also disrupted in the low micromolar range, comparable to that with CaM. While CaM predominates in regulating functional membrane anchorage of K-Ras, it has a very similar co-distribution with centrin1 on mitotic organelles. Given these results, a significant overlap of the CaM- and centrin1-dependent functions of K-Ras is suggested.

Functional genomics screening identifies aspartyl-tRNA synthetase as a novel prognostic marker and a therapeutic target for gastric cancers

Efficient molecular targeting therapies for most gastric cancers (GCs) are currently lacking, despite GC being one of the most frequent and often devastating malignancies worldwide. Thus, identification of novel therapeutic targets for GC is in high demand. Recent advancements of high-throughput nucleic acid synthesis methods combined with next-generation sequencing (NGS) platforms have made it feasible to conduct functional genomics screening using large-scale pooled lentiviral libraries aimed at discovering novel cancer therapeutic targets. In this study, we performed NGS-based functional genomics screening for human GC cell lines using an originally constructed 6,399 shRNA library targeting all 2,096 human metabolism genes. Our screening identified aspartyl-tRNA synthetase (DARS) as a possible candidate for a therapeutic target for GC. In-house tissue microarrays containing 346 cases of GC combined with public datasets showed that patients with high expression levels of DARS protein exhibited more advanced clinicopathologic parameters and a worse prognosis, specifically among diffuse-type GC patients. Both in vitro and in vivo experiments concretely evidenced that DARS inhibition achieved robust growth suppression of GC cells. Moreover, RNA sequencing of GC cell lines under shRNA-mediated DARS knockdown suggested that DARS inhibition exerts its effect through the inactivation of multiple p-ERK pathways. This MAPK-related growth suppression by DARS inhibition would also be applicable to other cancers; thus, it is warranted to investigate the expression and clinical significance of DARS in a wide spectrum of malignancies. Taken together, NGS-based high-throughput pooled lentiviral screening showed DARS as a novel prognostic marker and a promising therapeutic target for GC. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

Minerals and Cancer: Overview of the Possible Diagnostic Value

Simple Summary

Minerals are important but often overlooked compounds that are required for a variety of cellular biochemical processes and pathways that regulate cell proliferation. Their dietary imbalance, which is becoming more common in the diets of industrialized countries, is linked to an increased risk of cancer. The current review will present some of the most important minerals for human physiology and evaluate their potential application as cancer biomarkers.

Abstract

Cancer is the second leading cause of death worldwide and is expected to increase by one-third over the next two decades, in parallel with the growing proportion of the elderly population. Treatment and control of cancer incidence is a global issue. Since there is no clear way to prevent or cure this deadly malignancy, diagnostic, predictive, and prognostic markers for oncological diseases are of great therapeutic value. Minerals and trace elements are important micronutrients for normal physiological function of the body. They are abundant in natural food sources and are regularly included in dietary supplements whereas highly processed industrial food often contains reduced or altered amounts of them. In modern society, the daily intake, storage pools, and homeostasis of these micronutrients are dependent on certain dietary habits and can be thrown out of balance by malignancies. The current work summarizes the data on minerals and trace elements associated with abnormal accumulation or depletion states in tumor patients and discusses their value as potential tumor-associated biomarkers that could be introduced into cancer therapy.