scholarly journals Horizontal Transmission of Stress Resistance Genes Shape the Ecology of Beta- and Gamma-Proteobacteria

2021 ◽  
Vol 12 ◽  
Author(s):  
Shady Mansour Kamal ◽  
David J. Simpson ◽  
Zhiying Wang ◽  
Michael Gänzle ◽  
Ute Römling
Keyword(s):  
Core Genome ◽  
Protein Quality ◽  
Current Knowledge ◽  
Horizontal Transmission ◽  
Gene Products ◽  
Gamma Proteobacteria ◽  
Environmental Bacterium ◽  
Counter Selection ◽  
Distinct Sequence ◽  
Shock Proteins

The transmissible locus of stress tolerance (tLST) is found mainly in beta- and gamma-Proteobacteria and confers tolerance to elevated temperature, pressure, and chlorine. This genomic island, previously referred to as transmissible locus of protein quality control or locus of heat resistance likely originates from an environmental bacterium thriving in extreme habitats, but has been widely transmitted by lateral gene transfer. Although highly conserved, the gene content on the island is subject to evolution and gene products such as small heat shock proteins are present in several functionally distinct sequence variants. A number of these genes are xenologs of core genome genes with the gene products to widen the substrate spectrum and to be highly (complementary) expressed thus their functionality to become dominant over core genome genes. In this review, we will present current knowledge of the function of core tLST genes and discuss current knowledge on selection and counter-selection processes that favor maintenance of the tLST island, with frequent acquisition of gene products involved in cyclic di-GMP signaling, in different habitats from the environment to animals and plants, processed animal and plant products, man-made environments, and subsequently humans.

scholarly journals Why? – Successful Pseudomonas aeruginosa clones with a focus on clone C

2020 ◽  
Vol 44 (6) ◽  
pp. 740-762
Author(s):  
Changhan Lee ◽  
Jens Klockgether ◽  
Sebastian Fischer ◽  
Janja Trcek ◽  
Burkhard Tümmler ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Core Genome ◽  
Genomic Island ◽  
Protein Quality ◽  
Temperature Tolerance ◽  
Protein Homeostasis ◽  
Gene Products ◽  
Accessory Genome ◽  
The Core ◽  
Conserved Core

ABSTRACT The environmental species Pseudomonas aeruginosa thrives in a variety of habitats. Within the epidemic population structure of P. aeruginosa, occassionally highly successful clones that are equally capable to succeed in the environment and the human host arise. Framed by a highly conserved core genome, individual members of successful clones are characterized by a high variability in their accessory genome. The abundance of successful clones might be funded in specific features of the core genome or, although not mutually exclusive, in the variability of the accessory genome. In clone C, one of the most predominant clones, the plasmid pKLC102 and the PACGI-1 genomic island are two ubiquitous accessory genetic elements. The conserved transmissible locus of protein quality control (TLPQC) at the border of PACGI-1 is a unique horizontally transferred compository element, which codes predominantly for stress-related cargo gene products such as involved in protein homeostasis. As a hallmark, most TLPQC xenologues possess a core genome equivalent. With elevated temperature tolerance as a characteristic of clone C strains, the unique P. aeruginosa and clone C specific disaggregase ClpG is a major contributor to tolerance. As other successful clones, such as PA14, do not encode the TLPQC locus, ubiquitous denominators of success, if existing, need to be identified.

Cañihua (Chenopodium pallidicaule Aellen) a promising superfood in food industry: a review

2021 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Jerry Fredy Gomez Cahuata ◽  
Yessica Estefany Rosas-Quina ◽  
Erika Pachari Vera
Keyword(s):  
Food Industry ◽  
Unsaturated Fatty Acids ◽  
Protein Quality ◽  
Current Knowledge ◽  
Scientific Information ◽  
Essential Amino Acids ◽  
High Concentration ◽  
Content Type ◽  
Functional Value ◽  
Potential Applications

Purpose The purpose of this paper is to divulge the current knowledge about the nutritional and functional characteristics of Cañihua (Chenopodium pallidicaule Aellen), in addition to its potential applications in the food industry since research studies related to it are still limited compared to other cereals of greater diffusion. Design/methodology/approach The scientific information was collected from Web of Science, Scopus and Google Scholar databases, using keywords such as nutrition value of Chenopodium pallidicaule, amaranth and pseudocereals. Consistent information was selected according to its relevance, year of publication and accuracy with the topic. A total of 49 research papers were selected. Findings Cañihua is a grain with high nutritional potential, considered a superfood because it has a high protein quality, a balanced composition of essential amino acids and unsaturated fatty acids, with a high concentration of linoleic and oleic acid. Besides, it has a good level of bioactive compounds with high antioxidant capacity. However, its production and consumption are limited outside its area of origin, although its cultivation is possible under harsh conditions. Originality/value This paper, through a systematic bibliographic review, highlights the potential of cañihua to be considered in the development of food products with high nutritional and functional value. The information compiled will help researchers and professionals become aware of the importance of this grain and join forces in its processing and enhancement of its attributes.

scholarly journals Extracellular Chaperones as Novel Biomarkers of Overall Cancer Progression and Efficacy of Anticancer Therapy

2020 ◽  
Vol 10 (17) ◽  
pp. 6009
Author(s):  
Malgorzata Anna Krawczyk ◽  
Agata Pospieszynska ◽  
Małgorzata Styczewska ◽  
Ewa Bien ◽  
Sambor Sawicki ◽  
...  
Keyword(s):  
Cancer Progression ◽  
Current Knowledge ◽  
Therapeutic Targets ◽  
Age Group ◽  
Cancer Management ◽  
Novel Biomarkers ◽  
Immune System Regulation ◽  
New Biomarkers ◽  
Shock Proteins

Exosomal heat shock proteins (Hsps) are involved in intercellular communication both in physiological and pathological conditions. They play a role in key processes of carcinogenesis including immune system regulation, cell differentiation, vascular homeostasis and metastasis formation. Thus, exosomal Hsps are emerging biomarkers of malignancies and possible therapeutic targets. Adolescents and young adults (AYAs) are patients aged 15–39 years. This age group, placed between pediatric and adult oncology, pose a particular challenge for cancer management. New biomarkers of cancer growth and progression as well as prognostic factors are desperately needed in AYAs. In this review, we attempted to summarize the current knowledge on the role of exosomal Hsps in selected solid tumors characteristic for the AYA population and/or associated with poor prognosis in this age group. These included malignant melanoma, brain tumors, and breast, colorectal, thyroid, hepatocellular, lung and gynecological tract carcinomas. The studies on exosomal Hsps in these tumors are limited; however; some have provided promising results. Although further research is needed, there is potential for future clinical applications of exosomal Hsps in AYA cancers, both as novel biomarkers of disease presence, progression or relapse, or as therapeutic targets or tools for drug delivery.

scholarly journals Establishment and evaluation of a core genome multilocus sequence typing scheme for whole-genome sequence-based typing of Pseudomonas aeruginosa

2020 ◽  
pp. JCM.01987-20
Author(s):  
Hauke Tönnies ◽  
Karola Prior ◽  
Dag Harmsen ◽  
Alexander Mellmann
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Multilocus Sequence Typing ◽  
Core Genome ◽  
Target Genes ◽  
Multidrug Resistant ◽  
Population Based ◽  
Whole Genome Sequence ◽  
Nucleotide Polymorphisms ◽  
Environmental Bacterium ◽  
Random Dataset

The environmental bacterium Pseudomonas aeruginosa, in particular multidrug resistant clones, is often associated with nosocomial infections and outbreaks. Today, core genome multilocus sequence typing (cgMLST) is frequently applied to delineate sporadic cases from nosocomial transmissions. However, until recently, no cgMLST scheme for a standardized typing of P. aeruginosa was available.To establish a novel cgMLST scheme for P. aeruginosa, we initially determined the breadth of the P. aeruginosa population based on MLST data with a Bayesian approach (BAPS). Using genomic data of representative isolates for the whole population and for all 12 serogroups, we extracted target genes and further refined them using a random dataset of 1,000 P. aeruginosa genomes. Subsequently, we investigated reproducibility and discriminatory ability with repeatedly sequenced isolates and isolates from well-defined outbreak scenarios, respectively, and compared clustering applying two recently published cgMLST schemes.BAPS generated seven P. aeruginosa groups. To cover these and all serogroups, 15 reference strains were used to determine genes common in all strains. After refinement with the dataset of 1,000 genomes, the cgMLST scheme consisted of 3,867 target genes, which are representative for the P. aeruginosa population and highly reproducible using biological replicates. We finally evaluated the scheme by reanalyzing two published outbreaks, where the authors used single nucleotide polymorphisms (SNPs) typing. In both cases cgMLST was concordant to the previous SNP results and to the results of the two other cgMLST schemes.In conclusion, the highly-reproducible novel P. aeruginosa cgMLST scheme facilitates outbreak investigations due to the publicly available cgMLST nomenclature.

scholarly journals Revisiting Bap Multidomain Protein: More Than Sticking Bacteria Together

2020 ◽  
Vol 11 ◽  
Author(s):  
Jaione Valle ◽  
Xianyang Fang ◽  
Iñigo Lasa
Keyword(s):  
Biofilm Formation ◽  
Core Genome ◽  
Current Knowledge ◽  
Surface Proteins ◽  
Structure And Properties ◽  
Diverse Range ◽  
The Core ◽  
Self Assembling ◽  
Abiotic Surfaces ◽  
Range Of Functions

One of the major components of the staphylococcal biofilm is surface proteins that assemble as scaffold components of the biofilm matrix. Among the different surface proteins able to contribute to biofilm formation, this review is dedicated to the Biofilm Associated Protein (Bap). Bap is part of the accessory genome of Staphylococcus aureus but orthologs of Bap in other staphylococcal species belong to the core genome. When present, Bap promotes adhesion to abiotic surfaces and induces strong intercellular adhesion by self-assembling into amyloid like aggregates in response to the levels of calcium and the pH in the environment. During infection, Bap enhances the adhesion to epithelial cells where it binds directly to the host receptor Gp96 and inhibits the entry of the bacteria into the cells. To perform such diverse range of functions, Bap comprises several domains, and some of them include several motifs associated to distinct functions. Based on the knowledge accumulated with the Bap protein of S. aureus, this review aims to summarize the current knowledge of the structure and properties of each domain of Bap and their contribution to Bap functionality.

scholarly journals Aneuploidy and gene expression: is there dosage compensation?

Epigenomics ◽  
2019 ◽  
Vol 11 (16) ◽  
pp. 1827-1837 ◽  
Author(s):  
Shihoko Kojima ◽  
Daniela Cimini
Keyword(s):  
Gene Expression ◽  
Dosage Compensation ◽  
Current Knowledge ◽  
Gene Dosage ◽  
Congenital Defects ◽  
Gene Products ◽  
Epigenetic Changes ◽  
Transcript Levels ◽  
Compensation Mechanisms ◽  
Additional Chromosome

Aneuploidy (i.e., abnormal chromosome number) is the leading cause of miscarriage and congenital defects in humans. Moreover, aneuploidy is ubiquitous in cancer. The deleterious phenotypes associated with aneuploidy are likely a result of the imbalance in the levels of gene products derived from the additional chromosome(s). Here, we summarize the current knowledge on how the presence of extra chromosomes impacts gene expression. We describe studies that have found a strict correlation between gene dosage and transcript levels as wells as studies that have found a less stringent correlation, hinting at the possible existence of dosage compensation mechanisms. We conclude by peering into the epigenetic changes found in aneuploid cells and outlining current knowledge gaps and potential areas of future investigation.

Protein Quality Control Degradation in the Nucleus

2018 ◽  
Vol 87 (1) ◽  
pp. 725-749 ◽  
Author(s):  
Charisma Enam ◽  
Yifat Geffen ◽  
Tommer Ravid ◽  
Richard G. Gardner
Keyword(s):  
Quality Control ◽  
Protein Misfolding ◽  
Protein Quality ◽  
Current Knowledge ◽  
Protein Quality Control ◽  
Ubiquitin Proteasome System ◽  
Misfolded Proteins ◽  
Cellular Processes ◽  
Human Disorders ◽  
Protein Misfolding And Aggregation

Nuclear proteins participate in diverse cellular processes, many of which are essential for cell survival and viability. To maintain optimal nuclear physiology, the cell employs the ubiquitin-proteasome system to eliminate damaged and misfolded proteins in the nucleus that could otherwise harm the cell. In this review, we highlight the current knowledge about the major ubiquitin-protein ligases involved in protein quality control degradation (PQCD) in the nucleus and how they orchestrate their functions to eliminate misfolded proteins in different nuclear subcompartments. Many human disorders are causally linked to protein misfolding in the nucleus, hence we discuss major concepts that still need to be clarified to better understand the basis of the nuclear misfolded proteins’ toxic effects. Additionally, we touch upon potential strategies for manipulating nuclear PQCD pathways to ameliorate diseases associated with protein misfolding and aggregation in the nucleus.

scholarly journals Chaperoning STAT3/5 by Heat Shock Proteins: Interest of Their Targeting in Cancer Therapy

Cancers ◽  
2019 ◽  
Vol 12 (1) ◽  
pp. 21 ◽  
Author(s):  
Gaëtan Jego ◽  
François Hermetet ◽  
François Girodon ◽  
Carmen Garrido
Keyword(s):  
Heat Shock ◽  
Heat Shock Proteins ◽  
Cell Fate ◽  
Protein Quality ◽  
Immune Cell ◽  
Therapeutic Option ◽  
Specific Cell ◽  
Shock Proteins ◽  
Multicellular Organisms ◽  
Stat5 Transcription Factor

While cells from multicellular organisms are dependent upon exogenous signals for their survival, growth, and proliferation, commitment to a specific cell fate requires the correct folding and maturation of proteins, as well as the degradation of misfolded or aggregated proteins within the cell. This general control of protein quality involves the expression and the activity of molecular chaperones such as heat shock proteins (HSPs). HSPs, through their interaction with the STAT3/STAT5 transcription factor pathway, can be crucial both for the tumorigenic properties of cancer cells (cell proliferation, survival) and for the microenvironmental immune cell compartment (differentiation, activation, cytokine secretion) that contributes to immunosuppression, which, in turn, potentially promotes tumor progression. Understanding the contribution of chaperones such as HSP27, HSP70, HSP90, and HSP110 to the STAT3/5 signaling pathway has raised the possibility of targeting such HSPs to specifically restrain STAT3/5 oncogenic functions. In this review, we present how HSPs control STAT3 and STAT5 activation, and vice versa, how the STAT signaling pathways modulate HSP expression. We also discuss whether targeting HSPs is a valid therapeutic option and which HSP would be the best candidate for such a strategy.

scholarly journals The Roles of Ubiquitin-Binding Protein Shuttles in the Degradative Fate of Ubiquitinated Proteins in the Ubiquitin-Proteasome System and Autophagy

Cells ◽  
2019 ◽  
Vol 8 (1) ◽  
pp. 40 ◽  
Author(s):  
Katarzyna Zientara-Rytter ◽  
Suresh Subramani
Keyword(s):  
Protein Quality ◽  
Current Knowledge ◽  
Binding Protein ◽  
Ubiquitin Proteasome System ◽  
Oligomeric State ◽  
Receptor Associated Protein ◽  
Ubiquitin Proteasome ◽  
Specific Proteins ◽  
And Control ◽  
Recognition Code

The ubiquitin-proteasome system (UPS) and autophagy are the two major intracellular protein quality control (PQC) pathways that are responsible for cellular proteostasis (homeostasis of the proteome) by ensuring the timely degradation of misfolded, damaged, and unwanted proteins. Ubiquitination serves as the degradation signal in both these systems, but substrates are precisely targeted to one or the other pathway. Determining how and when cells target specific proteins to these two alternative PQC pathways and control the crosstalk between them are topics of considerable interest. The ubiquitin (Ub) recognition code based on the type of Ub-linked chains on substrate proteins was believed to play a pivotal role in this process, but an increasing body of evidence indicates that the PQC pathway choice is also made based on other criteria. These include the oligomeric state of the Ub-binding protein shuttles, their conformation, protein modifications, and the presence of motifs that interact with ATG8/LC3/GABARAP (autophagy-related protein 8/microtubule-associated protein 1A/1B-light chain 3/GABA type A receptor-associated protein) protein family members. In this review, we summarize the current knowledge regarding the Ub recognition code that is bound by Ub-binding proteasomal and autophagic receptors. We also discuss how cells can modify substrate fate by modulating the structure, conformation, and physical properties of these receptors to affect their shuttling between both degradation pathways.

scholarly journals Alzheimer Cells on Their Way to Derailment Show Selective Changes in Protein Quality Control Network

2020 ◽  
Vol 7 ◽  
Author(s):  
Margreet B. Koopman ◽  
Stefan G. D. Rüdiger
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Quality Control ◽  
Heat Shock ◽  
Heat Shock Proteins ◽  
Protein Quality ◽  
Protein Quality Control ◽  
Brain Regions ◽  
Control Network ◽  
Shock Proteins

Alzheimer’s Disease is driven by protein aggregation and is characterized by accumulation of Tau protein into neurofibrillary tangles. In healthy neurons the cellular protein quality control is successfully in charge of protein folding, which raises the question to which extent this control is disturbed in disease. Here, we describe that brain cells in Alzheimer’s Disease show very specific derailment of the protein quality control network. We performed a meta-analysis on the Alzheimer’s Disease Proteome database, which provides a quantitative assessment of disease-related proteome changes in six brain regions in comparison to age-matched controls. We noted that levels of all paralogs of the conserved Hsp90 chaperone family are reduced, while most other chaperones – or their regulatory co-chaperones - do not change in disease. The notable exception is a select group consisting of the stress inducible HSP70, its nucleotide exchange factor BAG3 – which links the Hsp70 system to autophagy - and neuronal small heat shock proteins, which are upregulated in disease. They are all members of a cascade controlled in the stress response, channeling proteins towards a pathway of chaperone assisted selective autophagy. Together, our analysis reveals that in an Alzheimer’s brain, with exception of Hsp90, the players of the protein quality control are still present in full strength, even in brain regions most severely affected in disease. The specific upregulation of small heat shock proteins and HSP70:BAG3, ubiquitous in all brain areas analyzed, may represent a last, unsuccessful attempt to advert cell death.

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