The genome streamlining theory suggests that reduction of microbial genome size optimizes energy utilization in stressful environments. Although this hypothesis has been explored in several cases of low-nutrient (oligotrophic) and high-temperature environments, little work has been carried out on microorganisms from low-pH environments, and what has been reported is inconclusive. In this study, we performed a large-scale comparative genomics investigation of more than 260 bacterial high-quality genome sequences of acidophiles, together with genomes of their closest phylogenetic relatives that live at circum-neutral pH. A statistically supported correlation is reported between reduction of genome size and decreasing pH that we demonstrate is due to gene loss and reduced gene sizes. This trend is independent from other genome size constraints such as temperature and G + C content. Genome streamlining in the evolution of acidophilic bacteria is thus supported by our results. The analyses of predicted Clusters of Orthologous Genes (COG) categories and subcellular location predictions indicate that acidophiles have a lower representation of genes encoding extracellular proteins, signal transduction mechanisms, and proteins with unknown function but are enriched in inner membrane proteins, chaperones, basic metabolism, and core cellular functions. Contrary to other reports for genome streamlining, there was no significant change in paralog frequencies across pH. However, a detailed analysis of COG categories revealed a higher proportion of genes in acidophiles in the following categories: "replication and repair," "amino acid transport," and "intracellular trafficking". This study brings increasing clarity regarding the genomic adaptations of acidophiles to life at low pH while putting elements, such as the reduction of average gene size, under the spotlight of streamlining theory. 

/pdf/a-large-scale-genome-based-survey-of-acidophilic-bacteria-1p8116y8.pdf

A Large-Scale Genome-Based Survey of Acidophilic Bacteria Suggests That Genome Streamlining Is an Adaption for Life at Low pH

Abstract The emergence of heterogeneous photocatalysis has facilitated redox reactions with high efficiency, without compromising the recyclability of the photocatalyst. Recently, stimuli‐responsive heterogeneous photocatalytic materials have emerged as a powerful synthetic tool, with simple and rapid recovery, as well as an enhanced dynamic control over reactions. Stimuli‐responsive polymers are often inexpensive and easy to produce. They can be switched from an active “on” state to an inert “off” state in response to external stimuli, allowing the production of photocatalyst with adaptability, recyclability, and orthogonal control on different chemical reactions. Despite this versatility, the application of artificial smart material in the field of heterogeneous photocatalysis has not yet been maximized. In this Minireview, we will examine the recent developments of this emerging class of stimuli‐responsive heterogeneous photocatalytic systems. We will discuss the synthesis route of appending photoactive components into different triggerable systems and, in particular, the controlled activation and recovery of the materials.

https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/anie.202211132

Temperature‐ and pH‐Responsive Polymeric Photocatalysts for Enhanced Control and Recovery

Characterization of a cytoplasmic 2-Cys peroxiredoxin from Citrus sinensis and its potential role in protection from oxidative damage and wound healing.

The influence of pH on the structure and stability of the Grb2 dimer reveals changes in the inter-domain and molecular interaction: Could it be a modulation mechanism?

Peroxiredoxin-4 supplementation modulates the immune response, shapes the intestinal microbiome, and enhances AHPND resistance in Penaeus vannamei.

Peroxiredoxin 6 (Prdx6), the ubiquitously expressed enzyme belonging to the family of peroxidases, namely, peroxiredoxins, exhibits a unique feature of functional compartmentalization within cells. Whereas, the enzyme localized in cytosol shows glutathione peroxidase activity, its lysosomal counterpart performs calcium independent phospholipase A2 (aiPLA2) activity. Like any true moonlighting protein, these two activities of Prdx6 are mutually exclusive of each other as a function of the pH of the cellular compartments. Differential substrate preference at different pH (i.e. peroxidised phospholipids at neutral pH and reduced phospholipids at acidic pH) is considered to be the reason for this behavior. To gain insight into the pH-induced structural–functional interplay we have systematically evaluated conformational variations, thermodynamic stability of the protein and quaternary state of the conformers at both pH 7.0 and 4.0. Our findings suggest that change in pH allows alterations in native states of Prdx6 at pH 7.0 and 4.0 such that the changes make the protein resistant to thermal denaturation at low pH.

/pdf/ph-induced-conformational-alteration-in-human-peroxiredoxin-5au5xs3j7w.pdf

Sunaina Hotumalani

Papers

pH induced conformational alteration in human peroxiredoxin 6 might be responsible for its resistance against lysosomal pH or high temperature.