scholarly journals Survival in Hostile Conditions: Pupylation and the Proteasome in Actinobacterial Stress Response Pathways

2021 ◽  
Vol 8 ◽  
Author(s):  
Tatjana von Rosen ◽  
Lena ML Keller ◽  
Eilika Weber-Ban
Keyword(s):  
Stress Responses ◽  
Protein Quality ◽  
Vital Role ◽  
Bacterial Protein ◽  
Core Particle ◽  
Free Living ◽  
Damage Response ◽  
Proteasomal Genes ◽  
Hexameric Atpase ◽  
Living Species

Bacteria employ a multitude of strategies to cope with the challenges they face in their natural surroundings, be it as pathogens, commensals or free-living species in rapidly changing environments like soil. Mycobacteria and other Actinobacteria acquired proteasomal genes and evolved a post-translational, ubiquitin-like modification pathway called pupylation to support their survival under rapidly changing conditions and under stress. The proteasomal 20S core particle (20S CP) interacts with ring-shaped activators like the hexameric ATPase Mpa that recruits pupylated substrates. The proteasomal subunits, Mpa and pupylation enzymes are encoded in the so-called Pup-proteasome system (PPS) gene locus. Genes in this locus become vital for bacteria to survive during periods of stress. In the successful human pathogen Mycobacterium tuberculosis, the 20S CP is essential for survival in host macrophages. Other members of the PPS and proteasomal interactors are crucial for cellular homeostasis, for example during the DNA damage response, iron and copper regulation, and heat shock. The multiple pathways that the proteasome is involved in during different stress responses suggest that the PPS plays a vital role in bacterial protein quality control and adaptation to diverse challenging environments.

scholarly journals Misinformation tactics protect rare birds from problem predators

2021 ◽  
Vol 7 (11) ◽  
pp. eabe4164
Author(s):  
Grant L. Norbury ◽  
Catherine J. Price ◽  
M. Cecilia Latham ◽  
Samantha J. Brown ◽  
A. David M. Latham ◽  
...  
Keyword(s):  
Decision Making ◽  
Threatened Species ◽  
Prey Availability ◽  
Free Living ◽  
Bird Populations ◽  
New Information ◽  
Mammalian Predators ◽  
Decision Making Processes ◽  
Living Species ◽  
Information Reliability

Efficient decision-making integrates previous experience with new information. Tactical use of misinformation can alter choice in humans. Whether misinformation affects decision-making in other free-living species, including problem species, is unknown. Here, we show that sensory misinformation tactics can reduce the impacts of predators on vulnerable bird populations as effectively as lethal control. We repeatedly exposed invasive mammalian predators to unprofitable bird odors for 5 weeks before native shorebirds arrived for nesting and for 8 weeks thereafter. Chick production increased 1.7-fold at odor-treated sites over 25 to 35 days, with doubled or tripled odds of successful hatching, resulting in a 127% increase in modeled population size in 25 years. We demonstrate that decision-making processes that respond to changes in information reliability are vulnerable to tactical manipulation by misinformation. Altering perceptions of prey availability offers an innovative, nonlethal approach to managing problem predators and improving conservation outcomes for threatened species.

scholarly journals Evolution, expression and functional analysis of cultivated allotetraploid cotton DIR genes

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zhengwen Liu ◽  
Xingfen Wang ◽  
Zhengwen Sun ◽  
Yan Zhang ◽  
Chengsheng Meng ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Rapid Evolution ◽  
Gene Clusters ◽  
Vital Role ◽  
Fiber Development ◽  
Rna Seq ◽  
Evolutionarily Conserved ◽  
Cell Wall Development ◽  
Tandem Duplications

Abstract Background Dirigent (DIR) proteins mediate regioselectivity and stereoselectivity during lignan biosynthesis and are also involved in lignin, gossypol and pterocarpan biosynthesis. This gene family plays a vital role in enhancing stress resistance and in secondary cell-wall development, but systematical understanding is lacking in cotton. Results In this study, 107 GbDIRs and 107 GhDIRs were identified in Gossypium barbadense and Gossypium hirsutum, respectively. Most of these genes have a classical gene structure without intron and encode proteins containing a signal peptide. Phylogenetic analysis showed that cotton DIR genes were classified into four distinct subfamilies (a, b/d, e, and f). Of these groups, DIR-a and DIR-e were evolutionarily conserved, and segmental and tandem duplications contributed equally to their formation. In contrast, DIR-b/d mainly expanded by recent tandem duplications, accompanying with a number of gene clusters. With the rapid evolution, DIR-b/d-III was a Gossypium-specific clade involved in atropselective synthesis of gossypol. RNA-seq data highlighted GhDIRs in response to Verticillium dahliae infection and suggested that DIR gene family could confer Verticillium wilt resistance. We also identified candidate DIR genes related to fiber development in G. barbadense and G. hirsutum and revealed their differential expression. To further determine the involvement of DIR genes in fiber development, we overexpressed a fiber length-related gene GbDIR78 in Arabidopsis and validated its function in trichomes and hypocotyls. Conclusions These findings contribute novel insights towards the evolution of DIR gene family and provide valuable information for further understanding the roles of DIR genes in cotton fiber development as well as in stress responses.

scholarly journals Ubiquitin-dependent switch during assembly of the proteasomal ATPases mediated by Not4 ubiquitin ligase

2018 ◽  
Vol 115 (52) ◽  
pp. 13246-13251 ◽  
Author(s):  
Xinyi Fu ◽  
Vladyslava Sokolova ◽  
Kristofor J. Webb ◽  
William Old ◽  
Soyeon Park
Keyword(s):  
Ubiquitin Ligase ◽  
Early Stage ◽  
E3 Ligase ◽  
Core Particle ◽  
Ubiquitinated Proteins ◽  
Ring Assembly ◽  
Hexameric Atpase

In the proteasome holoenzyme, the hexameric ATPases (Rpt1-Rpt6) enable degradation of ubiquitinated proteins by unfolding and translocating them into the proteolytic core particle. During early-stage proteasome assembly, individual Rpt proteins assemble into the hexameric “Rpt ring” through binding to their cognate chaperones: Nas2, Hsm3, Nas6, and Rpn14. Here, we show that Rpt ring assembly employs a specific ubiquitination-mediated control. An E3 ligase, Not4, selectively ubiquitinates Rpt5 during Rpt ring assembly. To access Rpt5, Not4 competes with Nas2 until the penultimate step and then with Hsm3 at the final step of Rpt ring completion. Using the known Rpt–chaperone cocrystal structures, we show that Not4-mediated ubiquitination sites in Rpt5 are obstructed by Nas2 and Hsm3. Thus, Not4 can distinguish a Rpt ring that matures without these chaperones, based on its accessibility to Rpt5. Rpt5 ubiquitination does not destabilize the ring but hinders incorporation of incoming subunits—Rpn1 ubiquitin receptor and Ubp6 deubiquitinase—thereby blocking progression of proteasome assembly and ubiquitin regeneration from proteasome substrates. Our findings reveal an assembly checkpoint where Not4 monitors chaperone actions during hexameric ATPase ring assembly, thereby ensuring the accuracy of proteasome holoenzyme maturation.

scholarly journals Expression of the Type VI Secretion System 1 Component Hcp1 Is Indirectly Repressed by OpaR inVibrio parahaemolyticus

2012 ◽  
Vol 2012 ◽  
pp. 1-7 ◽  
Author(s):  
Lizhi Ma ◽  
Yiquan Zhang ◽  
Xiaojuan Yan ◽  
Liping Guo ◽  
Li Wang ◽  
...  
Keyword(s):  
Quorum Sensing ◽  
Stress Responses ◽  
Structural Component ◽  
Vibrio Parahaemolyticus ◽  
Secretion System ◽  
Upstream Region ◽  
Bacterial Protein ◽  
Type Vi Secretion System ◽  
Type Vi Secretion ◽  
System 1

The type VI secretion system (T6SS) is bacterial protein injection machinery with roles in virulence, symbiosis, interbacterial interaction, antipathogenesis, and environmental stress responses. There are two T6SS loci, T6SS1 and T6SS2, in the two chromosomes ofVibrio parahaemolyticus, respectively. This work disclosed that the master quorum sensing (QS) regulator OpaR repressed the transcription ofhcp1encoding the structural component Hcp1 of T6SS1 inV. parahaemolyticus, indicating that QS had a negative regulatory action on T6SS1. A singleσ54-dependent promoter was transcribed forhcp1inV. parahaemolyticus, and its activity was repressed by the OpaR regulator. Since the OpaR protein could not bind to the upstream region ofhcp1, OpaR would repress the transcription ofhcp1in an indirect manner.

Allosteric Activation of HtrA Protease DegP by Stress Signals during Bacterial Protein Quality Control

2008 ◽  
Vol 47 (7) ◽  
pp. 1332-1334 ◽  
Author(s):  
Michael Meltzer ◽  
Sonja Hasenbein ◽  
Patrick Hauske ◽  
Nicolette Kucz ◽  
Melisa Merdanovic ◽  
...  
Keyword(s):  
Quality Control ◽  
Protein Quality ◽  
Protein Quality Control ◽  
Bacterial Protein ◽  
Allosteric Activation ◽  
Stress Signals

scholarly journals Draft Genome Sequence of Piscirickettsia litoralis , Isolated from Seawater

2016 ◽  
Vol 4 (6) ◽  
Author(s):  
Xuehua Wan ◽  
Alex J. Lee ◽  
Shaobin Hou ◽  
Blake Ushijima ◽  
Yen P. Nguyen ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Salmonid Fish ◽  
Draft Genome Sequence ◽  
Free Living ◽  
Living Species

One species of Piscirickettsia , a pathogen of salmonid fish, has been described. The genome sequence of a putative second and free-living species may provide insights into the evolution of pathogenicity in the genus.

scholarly journals Untangling the roles of parasites in food webs with generative network models

2015 ◽  
Author(s):  
Abigail Z. Jacobs ◽  
Jennifer A. Dunne ◽  
Cristopher Moore ◽  
Aaron Clauset
Keyword(s):  
Food Web ◽  
Food Webs ◽  
Statistical Physics ◽  
Network Models ◽  
Food Web Structure ◽  
Free Living ◽  
Web Structure ◽  
Living Species ◽  
Parasitic Interactions ◽  
The Impact

Food webs represent the set of consumer-resource interactions among a set of species that co-occur in a habitat, but most food web studies have omitted parasites and their interactions. Recent studies have provided conflicting evidence on whether including parasites changes food web structure, with some suggesting that parasitic interactions are structurally distinct from those among free-living species while others claim the opposite. Here, we describe a principled method for understanding food web structure that combines an efficient optimization algorithm from statistical physics called parallel tempering with a probabilistic generalization of the empirically well-supported food web niche model. This generative model approach allows us to rigorously estimate the degree to which interactions that involve parasites are statistically distinguishable from interactions among free-living species, whether parasite niches behave similarly to free-living niches, and the degree to which existing hypotheses about food web structure are naturally recovered. We apply this method to the well-studied Flensburg Fjord food web and show that while predation on parasites, concomitant predation of parasites, and parasitic intraguild trophic interactions are largely indistinguishable from free-living predation interactions, parasite-host interactions are different. These results provide a powerful new tool for evaluating the impact of classes of species and interactions on food web structure to shed new light on the roles of parasites in food webs.

scholarly journals Genome-wide analysis of BURP genes and identification of a BURP-V gene RcBURP4 in Rosachienesis

2021 ◽  
Author(s):  
Lufeng Fu ◽  
Zhujun Zhang ◽  
Hai Wang ◽  
Xiaojuan Zhao ◽  
Lin Su ◽  
...  
Keyword(s):  
Stress Responses ◽  
Light Response ◽  
Regulatory Elements ◽  
Vital Role ◽  
Severe Drought ◽  
Comprehensive Overview ◽  
Genome Database ◽  
Genome Wide ◽  
Bioinformatic Approaches ◽  
The Rose

Abstract BURP proteins are unique to plants and may contribute greatly to growth, development, and stress responses of plants. Despite the vital role of BURP proteins, little is known about these proteins in rose (Rosa spp.). In the present study, nine genes belonging to the BURP family in R. chienesis were identified by using multiple bioinformatic approaches against the rose genome database. The nine RcBURPs, with diverse structures, were located on all chromosomes of the rose genome, except for Chr2 and Chr3. Phylogenic analysis revealed that these RcBURPs can be classified into eight subfamilies, including BNM2-like, PG1β-like, USP-like, RD22-like, BURP-V, BURP-VI, BURP-VII, and BURP-VIII. Conserved motif and exon-intron analyses indicated a conserved pattern within the same subfamily. The presumed cis-regulatory elements (CREs) within the promoter region of each RcBURP were analyzed and the results showed that all RcBURPs contained different types of CREs, including abiotic stress-, light response-, phytohormones response-, and plant growth and development-related CREs. Transcriptomic analysis revealed that a BURP-V member, RcBURP4, was induced in rose leaves and roots under mild and severe drought treatments. We then overexpressed RcBURP4 in Arabidopsis and examined its role under abscisic acid (ABA), NaCl, polyethylene glycol (PEG), and drought treatments. Furthermore, RcBURP4-silenced rose plants exhibited decreased tolerance to dehydration. The results obtained from this study provide the first comprehensive overview of RcBURPs and highlight the importance of RcBURP4 in rose plant.

scholarly journals What factors explain the geographical range of mammalian parasites?

2019 ◽  
Vol 286 (1903) ◽  
pp. 20190673 ◽  
Author(s):  
James E. Byers ◽  
J. P. Schmidt ◽  
Paula Pappalardo ◽  
Sarah E. Haas ◽  
Patrick R. Stephens
Keyword(s):  
Host Species ◽  
Parasite Species ◽  
Geographical Area ◽  
Complete Information ◽  
Sampling Effort ◽  
Free Living ◽  
Living Species ◽  
Habitat Breadth ◽  
Taxonomic Groups ◽  
Host Characteristics

Free-living species vary substantially in the extent of their spatial distributions. However, distributions of parasitic species have not been comprehensively compared in this context. We investigated which factors most influence the geographical extent of mammal parasites. Using the Global Mammal Parasite Database we analysed 17 818 individual geospatial records on 1806 parasite species (encompassing viruses, bacteria, protozoa, arthropods and helminths) that infect 396 carnivore, ungulate and primate host species. As a measure of the geographical extent of each parasite species we quantified the number and area of world ecoregions occupied by each. To evaluate the importance of variables influencing the summed area of ecoregions occupied by a parasite species, we used Bayesian network analysis of a subset ( n = 866) of the parasites in our database that had at least two host species and complete information on parasite traits. We found that parasites that covered more geographical area had a greater number of host species, higher average phylogenetic relatedness between host species and more sampling effort. Host and parasite taxonomic groups had weak and indirect effects on parasite ecoregion area; parasite transmission mode had virtually no effect. Mechanistically, a greater number of host species probably increases both the collective abundance and habitat breadth of hosts, providing more opportunities for a parasite to have an expansive range. Furthermore, even though mammals are one of the best-studied animal classes, the ecoregion area occupied by their parasites is strongly sensitive to sampling effort, implying mammal parasites are undersampled. Overall, our results support that parasite geographical extent is largely controlled by host characteristics, many of which are subsumed within host taxonomic identity.

Phase morphs and phoresy: New species of Antennoseius (Vitzthumia) mites (Acari: Mesostigmata: Ascidae) associated with pyrophilous carabids (Carabidae: Sericoda spp.) in Alberta, Canada

Zootaxa ◽  
2008 ◽  
Vol 1961 (1) ◽  
pp. 37-57 ◽  
Author(s):  
FRÉDÉRIC BEAULIEU ◽  
ANDREA D. DÉCHÊNE ◽  
DAVID E. WALTER
Keyword(s):  
New Species ◽  
North American ◽  
North American Species ◽  
Carabid Beetles ◽  
Free Living ◽  
Adult Females ◽  
As Species ◽  
Laboratory Cultures ◽  
Living Species ◽  
Mite Genus

The mite genus Antennoseius is composed of free-living species in soil and litter, as well as species that are phoretic on carabid beetles as adult females. Among approximately 60 described Antennoseius species, one North American species, A. janus, was found in laboratory cultures to have two female morphs: one granular, free-living morph, and one smooth, putatively phoretic morph. We here describe the adult females of A. perseus n. sp. and A. pyrophilus n. sp. collected from under the elytra of carabid beetles (Sericoda quadripunctata and S. bembidioides) associated with recently burned forests in Alberta, Canada. We also describe the female and male of a distinct, granular, non-phoretic morph of A. perseus, obtained from soil and by rearing the offspring of phoretic females. A key to the females of Antennoseius species having an ambulacrum on leg I (i.e. subgenus Vitzthumia) is provided.

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