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Jetty van Ginkel, Mike Filius, Malwina Szczepaniak, Pawel Tulinski, Anne S Meyer, Chirlmin Joo
Proteomic analyses provide essential information on molecular pathways of cellular systems and the state of a living organism. Mass spectrometry is currently the first choice for proteomic analysis. However, the requirement for a large amount of sample renders a small-scale proteomics study challenging. Here, we demonstrate a proof of concept of single-molecule FRET-based protein fingerprinting. We harnessed the AAA+ protease ClpXP to scan peptides. By using donor fluorophore-labeled ClpP, we sequentially read out FRET signals from acceptor-labeled amino acids of peptides...
March 12, 2018: Proceedings of the National Academy of Sciences of the United States of America
Elizabeth Reed, Christina M Ferreira, Rebecca Bell, Eric W Brown, Jie Zheng
Microgreens, like sprouts, are relatively fast growing, and generally consumed raw. Moreover, as observed in sprouts, microbial contamination from preharvest sources could also be present in the production of microgreens. In this study, two Salmonella enterica serovars (Hartford and Cubana) applied, at multiple inoculation levels, were evaluated for survival and growth on alfalfa sprouts and Swiss chard microgreens using the most probable number (MPN) method. Various abiotic factors were also examined for their effects on Salmonella survival and growth on sprouts and microgreens...
February 16, 2018: Applied and Environmental Microbiology
Andrew W Tanner, Valerie J Carabetta, David Dubnau
In Bacillus subtilis, a proteolytic machine composed of MecA, ClpC and ClpP degrades the transcription factor ComK, controlling its accumulation during growth. MecA also inhibits sporulation and biofilm formation by down-regulating spoIIG and sinI, genes that are dependent for their transcription on the phosphorylated protein Spo0A-P. Additionally, MecA has been shown to interact in vitro with Spo0A. Although the inhibitory effect on transcription requires MecA's binding partner ClpC, inhibition is not accompanied by the degradation of Spo0A, pointing to a previously unsuspected regulatory mechanism involving these proteins...
February 15, 2018: Molecular Microbiology
Shylesh Bhaskaran, Gavin Pharaoh, Rojina Ranjit, Ashley Murphy, Satoshi Matsuzaki, Binoj C Nair, Brittany Forbes, Suzana Gispert, Georg Auburger, Kenneth M Humphries, Michael Kinter, Timothy M Griffin, Sathyaseelan S Deepa
Caseinolytic peptidase P (ClpP) is a mammalian quality control protease that is proposed to play an important role in the initiation of the mitochondrial unfolded protein response (UPRmt), a retrograde signaling response that helps to maintain mitochondrial protein homeostasis. Mitochondrial dysfunction is associated with the development of metabolic disorders, and to understand the effect of a defective UPRmt on metabolism, ClpP knockout (ClpP-/-) mice were analyzed. ClpP-/- mice fed ad libitum have reduced adiposity and paradoxically improved insulin sensitivity...
February 2, 2018: EMBO Reports
Brittany D Bennett, Kaitlyn E Redford, Jeffrey A Gralnick
Shewanella oneidensis strain MR-1 is a versatile bacterium capable of respiring extracellular, insoluble ferric oxide minerals under anaerobic conditions. The respiration of iron minerals results in the production of soluble ferrous ions, which at high concentrations are toxic to living organisms. It is not fully understood how Fe2+ is toxic to cells anaerobically; nor is it fully understood how S. oneidensis is able to resist high levels of Fe2+ Here we describe the results of a transposon-mutant screen and subsequent deletion of the genes clpX and clpP in S...
January 29, 2018: Journal of Bacteriology
Minghui Yan, Peter W Fritsch, Michael J Moore, Tao Feng, Aiping Meng, Jing Yang, Tao Deng, Congxiao Zhao, Xiaohong Yao, Hang Sun, Hengchang Wang
Relationships among the genera of the small, woody family Styracaceae and among families of the large, diverse order Ericales have resisted complete resolution with sequences from one or a few genes. We used plastome sequencing to attempt to resolve the backbone relationships of Styracaceae and Ericales and to explore plastome structural evolution. Complete plastomes for 23 species are newly reported here, including 18 taxa of Styracaceae and five of Ericales (including species of Sapotaceae, Clethraceae, Symplocaceae, and Diapensiaceae)...
January 19, 2018: Molecular Phylogenetics and Evolution
Lei He, Hongwei Meng, Qian Liu, Mo Hu, Yanan Wang, Xiaoying Chen, Xiaoyun Liu, Min Li
Background: Staphylococcus aureus (S. aureus or SA) is a leading cause of healthcare-associated (HA-) and community-associated (CA) infection. HA-SA isolates usually cause nosocomial pneumonia, bloodstream infections, catheter-related urinary tract infections, etc. On the other hand, CA-SA isolates usually cause highly fatal diseases, such as SSTIs as well as post influenza necrotic hemorrhagic pneumonia. The differences of the infection types are partially due to the unique characteristics between HA-SA and CA-SA isolates...
2018: Clinical Proteomics
Liang Zhang, Tao Lyu, Yang Zhang, Mark Button, Carlos A Arias, Kela P Weber, Hans Brix, Pedro N Carvalho
Microbial degradation is an important pathway during the removal of pharmaceuticals in constructed wetlands (CWs). However, the effects of CW design, plant presence, and different plant species on the microbial community in CWs have not been fully explored. This study aims to investigate the microbial community metabolic function of different types of CWs used to treat ibuprofen via community-level physiological profiling (CLPP) analysis. We studied the interactions between three CW designs (unsaturated, saturated and aerated) and six types of mesocosms (one unplanted and five planted, with Juncus, Typha, Berula, Phragmites and Iris) treating synthetic wastewater...
December 23, 2017: Water Research
Abdulmoein Eid Al-Agha, Ihab Abdulhamed Ahmed, Esther Nuebel, Mika Moriwaki, Barry Moore, Katherine A Peacock, Tim Mosbruger, Deborah W Neklason, Lynn B Jorde, Mark Yandell, Corrine K Welt
Context: The etiology of primary ovarian insufficiency (POI) remains unknown in a majority of cases. Objective: We sought to identify genes causing POI. Design: The study was a familial genetic study. Setting: The study was performed in two academic institutions. Patients: We identified a consanguineous Yemeni family in which 4 daughters had POI. A brother had azoospermia. Intervention: DNA was subjected to whole genome sequencing...
December 12, 2017: Journal of Clinical Endocrinology and Metabolism
Rika Kosaki, Reiko Horikawa, Eriko Fujii, Kenjiro Kosaki
Perrault syndrome represents a genetically heterogeneous disorder characterized by sensorineural hearing loss in males and females and ovarian dysfunction in females. Causative genes include HARS2, HSD17B4, CLPP, C10orf2, and LARS2. Some patients with Perrault syndrome exhibit neurologic features including learning disability, cerebellar ataxia, and peripheral neuropathy and are classified as type 2 and are clinically separate from those without neurological symptoms other than a hearing loss (type 1). To date, all reported patients with LARS2 mutations (15 patients in 8 families) have been classified as type 1...
February 2018: American Journal of Medical Genetics. Part A
(no author information available yet)
Proteolysis is essential for all living organisms to maintain the protein homeostasis and to adapt to changing environmental conditions. ClpP is the main protease in Bacillus subtilis , and forms complexes with different Clp ATPases. These complexes play crucial roles during heat stress, but also in sporulation or cell morphology. Especially enzymes of cell wall-, amino acid-, and nucleic acid biosynthesis are known substrates of the protease ClpP during glucose starvation. The aim of this study was to analyze the influence of a clpP mutation on the metabolism in different growth phases and to search for putative new ClpP substrates...
November 24, 2017: Metabolites
Adrian C D Fuchs, Lorena Maldoner, Katharina Hipp, Marcus D Hartmann, Jörg Martin
Eukaryotic and archaeal proteasomes are paradigms for self-compartmentalizing proteases. To a large extent, their function requires interplay with hexameric ATPases associated with diverse cellular activities (AAA+) that act as substrate unfoldases. Bacteria have various types of self-compartmentalizing proteases; in addition to the proteasome itself, these include the proteasome homolog HslV, which functions together with the AAA+ HslU; the ClpP protease with its partner AAA+ ClpX; and Anbu, a recently characterized ancestral proteasome variant...
January 19, 2018: Journal of Biological Chemistry
Sejeong Kim, Jiyeon Jeong, Heeyoung Lee, Jeeyeon Lee, Soomin Lee, Jimyeong Ha, Yukyoung Choi, Yohan Yoon, Kyoung-Hee Choi
This study was conducted to examine the kinetic behavior of Campylobacter jejuni in raw beef tartare by using mathematical models and to identify genes related to C. jejuni survival at cold temperatures. C. jejuni was inoculated onto beef tartare samples, stored at 4, 10, 15, 25, and 30°C, plated on modified charcoal-cefoperazone-deoxycholate agar, and enumerated. The survival data was fitted to the Weibull model to calculate delta (δ), which is the time required for the first 1-log reduction of the cells...
December 2017: Journal of Food Protection
Marta Carroni, Kamila B Franke, Michael Maurer, Jasmin Jäger, Ingo Hantke, Felix Gloge, Daniela Linder, Sebastian Gremer, Kürşad Turgay, Bernd Bukau, Axel Mogk
Ring-forming AAA+ chaperones exert ATP-fueled substrate unfolding by threading through a central pore. This activity is potentially harmful requiring mechanisms for tight repression and substrate-specific activation. The AAA+ chaperone ClpC with the peptidase ClpP forms a bacterial protease essential to virulence and stress resistance. The adaptor MecA activates ClpC by targeting substrates and stimulating ClpC ATPase activity. We show how ClpC is repressed in its ground state by determining ClpC cryo-EM structures with and without MecA...
November 22, 2017: ELife
Yangxiong Li, Nathan P Lavey, Jesse A Coker, Jessica E Knobbe, Dat C Truong, Hongtao Yu, Yu-Shan Lin, Susan L Nimmo, Adam S Duerfeldt
The acyldepsipeptide (ADEP) antibiotics operate through a clinically unexploited mechanism of action and thus have attracted attention from several antibacterial development groups. The ADEP scaffold is synthetically tractable, and deep-seated modifications have produced extremely potent antibacterial leads against Gram-positive pathogens. Although newly identified ADEP analogs demonstrate remarkable antibacterial activity against bacterial isolates and in mouse models of bacterial infections, stability issues pertaining to the depsipeptide core remain...
November 9, 2017: ACS Medicinal Chemistry Letters
Justin M Miller, Hamza Chaudhary, Justin D Marsee
Regulated proteolysis is required in all organisms for the removal of misfolded or degradation-tagged protein substrates in cellular quality control pathways. The molecular machines that catalyze this process are known as ATP-dependent proteases with examples that include ClpAP and ClpCP. Clp/Hsp100 subunits form ring-structures that couple the energy of ATP binding and hydrolysis to protein unfolding and subsequent translocation of denatured protein into the compartmentalized ClpP protease for degradation...
November 9, 2017: Journal of Structural Biology
Meng Wu, Guilong Li, Xiaofen Chen, Jia Liu, Ming Liu, Chunyu Jiang, Zhongpei Li
Chlorantraniliprole (CAP) is a newly developed insecticide widely used in rice fields in China. There have been few studies regarding its effects on soil microbial functional diversity and bacterial community composition. An 85-day microcosm experiment was performed to reveal the dissipation dynamics of CAP under different application doses in a silty-loam paddy soil in subtropical China. The half-life of CAP was 51.3 and 62.5d for low (1mgkg(-1)) and high (10mgkg(-1)) application dose, respectively. We used a combination of community level physiological profile (CLPP) and 16S rRNA gene sequencing analysis to get insights into the soil microbial features responded to CAP during the experiment...
November 5, 2017: Science of the Total Environment
Péter Poczai, Jaakko Hyvönen
Spanish moss (Tillandsia usneoides) is an epiphytic bromeliad widely distributed throughout tropical and warm temperate America. This plant is highly adapted to extreme environmental conditions. Striking features of this species include specialized trichomes (scales) covering the surface of its shoots aiding the absorption of water and nutrients directly from the atmosphere and a specific photosynthesis using crassulacean acid metabolism (CAM). Here we report the plastid genome of Spanish moss and present the comparison of genome organization and sequence evolution within Poales...
2017: PloS One
Jian Zhang, Jianwei Xiao, Yuqian Li, Bodan Su, Huimin Xu, Xiaoyi Shan, Chengwei Song, Jianbo Xie, Ruili Li
The chloroplast, as the photosynthetic organelle of plants, plays a crucial role in plant development. Extensive studies have been conducted on chloroplast development; however, the related regulatory mechanism still remains elusive. Here, we characterized a mutant with defective chloroplasts in Arabidopsis, termed pigment-defective mutant3 (pdm3), which exhibits a distinct albino phenotype in leaves, eventually leading to pdm3 seedling lethality under autotrophic growth conditions. Electron microscopy demonstrated that the number of thylakoids was reduced and the structure of those thylakoids was disrupted in the pdm3 mutant, which eventually led to the breakdown of chloroplasts...
November 28, 2017: Journal of Experimental Botany
Zhitao Niu, Jiajia Pan, Shuying Zhu, Ludan Li, Qingyun Xue, Wei Liu, Xiaoyu Ding
Apostasioideae, consists of only two genera, Apostasia and Neuwiedia, which are mainly distributed in Southeast Asia and northern Australia. The floral structure, taxonomy, biogeography, and genome variation of Apostasioideae have been intensively studied. However, detailed analyses of plastome composition and structure and comparisons with those of other orchid subfamilies have not yet been conducted. Here, the complete plastome sequences of Apostasia wallichii and Neuwiedia singapureana were sequenced and compared with 43 previously published photosynthetic orchid plastomes to characterize the plastome structure and evolution in the orchids...
2017: Frontiers in Plant Science
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