Chapter 9. Evolution of Viral Capsid Structures – the Three Domains of Life

AbstractThe deep biosphere contains members from all three domains of life along with viruses. Here we investigate the deep terrestrial virosphere by sequencing community nucleic acids from three groundwaters of contrasting chemistries, origins, and ages. These viromes constitute a highly unique community compared to other environmental viromes and sequenced viral isolates. Viral host prediction suggests that many of the viruses are associated with Firmicutes and Patescibacteria, a superphylum lacking previously described active viruses. RNA transcript-based activity implies viral predation in the shallower marine water-fed groundwater, while the deeper and more oligotrophic waters appear to be in ‘metabolic standby’. Viral encoded antibiotic production and resistance systems suggest competition and antagonistic interactions. The data demonstrate a viral community with a wide range of predicted hosts that mediates nutrient recycling to support a higher microbial turnover than previously anticipated. This suggests the presence of ‘kill-the-winner’ oscillations creating slow motion ‘boom and burst’ cycles.

Download Full-text

Lipoproteins Are Responsible for the Pro-Inflammatory Property of Staphylococcus aureus Extracellular Vesicles

International Journal of Molecular Sciences ◽

10.3390/ijms22137099 ◽

2021 ◽

Vol 22 (13) ◽

pp. 7099

Author(s):

Pradeep Kumar Kopparapu ◽

Meghshree Deshmukh ◽

Zhicheng Hu ◽

Majd Mohammad ◽

Marco Maugeri ◽

...

Keyword(s):

Extracellular Vesicles ◽

Inflammatory Responses ◽

Surface Proteins ◽

Host Cells ◽

Immune Stimulation ◽

Domains Of Life ◽

Major Surface ◽

Staphylococcal Aureus

Staphylococcal aureus (S. aureus), a Gram-positive bacteria, is known to cause various infections. Extracellular vesicles (EVs) are a heterogeneous array of membranous structures secreted by cells from all three domains of life, i.e., eukaryotes, bacteria, and archaea. Bacterial EVs are implied to be involved in both bacteria–bacteria and bacteria–host interactions during infections. It is still unclear how S. aureus EVs interact with host cells and induce inflammatory responses. In this study, EVs were isolated from S. aureus and mutant strains deficient in either prelipoprotein lipidation (Δlgt) or major surface proteins (ΔsrtAB). Their immunostimulatory capacities were assessed both in vitro and in vivo. We found that S. aureus EVs induced pro-inflammatory responses both in vitro and in vivo. However, this activity was dependent on lipidated lipoproteins (Lpp), since EVs isolated from the Δlgt showed no stimulation. On the other hand, EVs isolated from the ΔsrtAB mutant showed full immune stimulation, indicating the cell wall anchoring of surface proteins did not play a role in immune stimulation. The immune stimulation of S. aureus EVs was mediated mainly by monocytes/macrophages and was TLR2 dependent. In this study, we demonstrated that not only free Lpp but also EV-imbedded Lpp had high pro-inflammatory activity.

Download Full-text

A Global Review on Short Peptides: Frontiers and Perspectives

Molecules ◽

10.3390/molecules26020430 ◽

2021 ◽

Vol 26 (2) ◽

pp. 430

Author(s):

Vasso Apostolopoulos ◽

Joanna Bojarska ◽

Tsun-Thai Chai ◽

Sherif Elnagdy ◽

Krzysztof Kaczmarek ◽

...

Keyword(s):

Protein Interactions ◽

Targeted Delivery ◽

Swot Analysis ◽

Functional Materials ◽

Great Promise ◽

Short Peptides ◽

Altered Peptide Ligands ◽

Short Peptide ◽

Domains Of Life

Peptides are fragments of proteins that carry out biological functions. They act as signaling entities via all domains of life and interfere with protein-protein interactions, which are indispensable in bio-processes. Short peptides include fundamental molecular information for a prelude to the symphony of life. They have aroused considerable interest due to their unique features and great promise in innovative bio-therapies. This work focusing on the current state-of-the-art short peptide-based therapeutical developments is the first global review written by researchers from all continents, as a celebration of 100 years of peptide therapeutics since the commencement of insulin therapy in the 1920s. Peptide “drugs” initially played only the role of hormone analogs to balance disorders. Nowadays, they achieve numerous biomedical tasks, can cross membranes, or reach intracellular targets. The role of peptides in bio-processes can hardly be mimicked by other chemical substances. The article is divided into independent sections, which are related to either the progress in short peptide-based theranostics or the problems posing challenge to bio-medicine. In particular, the SWOT analysis of short peptides, their relevance in therapies of diverse diseases, improvements in (bio)synthesis platforms, advanced nano-supramolecular technologies, aptamers, altered peptide ligands and in silico methodologies to overcome peptide limitations, modern smart bio-functional materials, vaccines, and drug/gene-targeted delivery systems are discussed.

Download Full-text

Functional expression of the eukaryotic proton pump rhodopsin OmR2 in Escherichia coli and its photochemical characterization

Scientific Reports ◽

10.1038/s41598-021-94181-w ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Masuzu Kikuchi ◽

Keiichi Kojima ◽

Shin Nakao ◽

Susumu Yoshizawa ◽

Shiho Kawanishi ◽

...

Keyword(s):

Escherichia Coli ◽

Proton Pump ◽

Expression System ◽

Spectroscopic Characterization ◽

Functional Expression ◽

Proton Pumping ◽

E Coli ◽

Oxyrrhis Marina ◽

Domains Of Life

AbstractMicrobial rhodopsins are photoswitchable seven-transmembrane proteins that are widely distributed in three domains of life, archaea, bacteria and eukarya. Rhodopsins allow the transport of protons outwardly across the membrane and are indispensable for light-energy conversion in microorganisms. Archaeal and bacterial proton pump rhodopsins have been characterized using an Escherichia coli expression system because that enables the rapid production of large amounts of recombinant proteins, whereas no success has been reported for eukaryotic rhodopsins. Here, we report a phylogenetically distinct eukaryotic rhodopsin from the dinoflagellate Oxyrrhis marina (O. marina rhodopsin-2, OmR2) that can be expressed in E. coli cells. E. coli cells harboring the OmR2 gene showed an outward proton-pumping activity, indicating its functional expression. Spectroscopic characterization of the purified OmR2 protein revealed several features as follows: (1) an absorption maximum at 533 nm with all-trans retinal chromophore, (2) the possession of the deprotonated counterion (pKa = 3.0) of the protonated Schiff base and (3) a rapid photocycle through several distinct photointermediates. Those features are similar to those of known eukaryotic proton pump rhodopsins. Our successful characterization of OmR2 expressed in E. coli cells could build a basis for understanding and utilizing eukaryotic rhodopsins.

Download Full-text

Identification of Biomolecules Involved in the Adaptation to the Environment of Cold-Loving Microorganisms and Metabolic Pathways for Their Production

Biomolecules ◽

10.3390/biom11081155 ◽

2021 ◽

Vol 11 (8) ◽

pp. 1155

Author(s):

Eva Garcia-Lopez ◽

Paula Alcazar ◽

Cristina Cid

Keyword(s):

Metabolic Pathways ◽

Extracellular Polymeric Substances ◽

Molecular Mechanisms ◽

Current Knowledge ◽

Analytical Techniques ◽

Light Protection ◽

Domains Of Life ◽

Mechanisms Of Adaptation ◽

Resistance To Stress ◽

Function Discovery

Cold-loving microorganisms of all three domains of life have unique and special abilities that allow them to live in harsh environments. They have acquired structural and molecular mechanisms of adaptation to the cold that include the production of anti-freeze proteins, carbohydrate-based extracellular polymeric substances and lipids which serve as cryo- and osmoprotectants by maintaining the fluidity of their membranes. They also produce a wide diversity of pigmented molecules to obtain energy, carry out photosynthesis, increase their resistance to stress and provide them with ultraviolet light protection. Recently developed analytical techniques have been applied as high-throughoutput technologies for function discovery and for reconstructing functional networks in psychrophiles. Among them, omics deserve special mention, such as genomics, transcriptomics, proteomics, glycomics, lipidomics and metabolomics. These techniques have allowed the identification of microorganisms and the study of their biogeochemical activities. They have also made it possible to infer their metabolic capacities and identify the biomolecules that are parts of their structures or that they secrete into the environment, which can be useful in various fields of biotechnology. This Review summarizes current knowledge on psychrophiles as sources of biomolecules and the metabolic pathways for their production. New strategies and next-generation approaches are needed to increase the chances of discovering new biomolecules.

Download Full-text

Captivating Perplexities of Spinareovirinae 5′ RNA Caps

Viruses ◽

10.3390/v13020294 ◽

2021 ◽

Vol 13 (2) ◽

pp. 294

Author(s):

Justine Kniert ◽

Qi Feng Lin ◽

Maya Shmulevitz

Keyword(s):

Immune Recognition ◽

Domains Of Life ◽

The Many ◽

Rna Capping ◽

Multiple Domains ◽

Rna Caps

RNAs with methylated cap structures are present throughout multiple domains of life. Given that cap structures play a myriad of important roles beyond translation, such as stability and immune recognition, it is not surprising that viruses have adopted RNA capping processes for their own benefit throughout co-evolution with their hosts. In fact, that RNAs are capped was first discovered in a member of the Spinareovirinae family, Cypovirus, before these findings were translated to other domains of life. This review revisits long-past knowledge and recent studies on RNA capping among members of Spinareovirinae to help elucidate the perplex processes of RNA capping and functions of RNA cap structures during Spinareovirinae infection. The review brings to light the many uncertainties that remain about the precise capping status, enzymes that facilitate specific steps of capping, and the functions of RNA caps during Spinareovirinae replication.

Download Full-text

Scarcity of scale-free topology is universal across biochemical networks

Scientific Reports ◽

10.1038/s41598-021-85903-1 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Harrison B. Smith ◽

Hyunju Kim ◽

Sara I. Walker

Keyword(s):

Large Body ◽

Biochemical Networks ◽

Biological Organization ◽

Scale Free ◽

Levels Of Organization ◽

Common Structure ◽

Domains Of Life ◽

Ecosystem Level ◽

Different Levels ◽

Organizing Principles

AbstractBiochemical reactions underlie the functioning of all life. Like many examples of biology or technology, the complex set of interactions among molecules within cells and ecosystems poses a challenge for quantification within simple mathematical objects. A large body of research has indicated many real-world biological and technological systems, including biochemistry, can be described by power-law relationships between the numbers of nodes and edges, often described as “scale-free”. Recently, new statistical analyses have revealed true scale-free networks are rare. We provide a first application of these methods to data sampled from across two distinct levels of biological organization: individuals and ecosystems. We analyze a large ensemble of biochemical networks including networks generated from data of 785 metagenomes and 1082 genomes (sampled from the three domains of life). The results confirm no more than a few biochemical networks are any more than super-weakly scale-free. Additionally, we test the distinguishability of individual and ecosystem-level biochemical networks and show there is no sharp transition in the structure of biochemical networks across these levels of organization moving from individuals to ecosystems. This result holds across different network projections. Our results indicate that while biochemical networks are not scale-free, they nonetheless exhibit common structure across different levels of organization, independent of the projection chosen, suggestive of shared organizing principles across all biochemical networks.

Download Full-text