DOCSLIB.ORG

(12) United States Patent (10) Patent No.: US 9,353,359 B2 Sorek Et Al

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
(12) United States Patent (10) Patent No.: US 9,353,359 B2 Sorek Et Al US009353359B2 (12) United States Patent (10) Patent No.: US 9,353,359 B2 Sorek et al. (45) Date of Patent: May 31, 2016 (54) BACTERIAL ANTI-PHAGE DEFENSE OTHER PUBLICATIONS SYSTEMS Copeland et al. 2007; Complete sequence of Pseudomonus (71) Applicant: Yeda Research and Development Co. mendocinaymp. EMBL: ABP83335.* Ltd., Rehovot (IL) Lucas et al. 2008; Complete sequence of Acidithiobacillus fer rooxidans ATCC 53993. EMBL: ACH83539.1. (72) Inventors: Rotem Sorek, Rehovot (IL); Hila Kerfeld et al. 2009; Complete sequence of plasmid of Amonifex Sberro, Rehovot (IL): Azita Leavitt, degensii KC4, EMBL: ACX53253.1.* Rehovot (IL) Lee et al. 2006; Sequence analysis of two cryptic plasmids from Bifidobacterium longump.O10A and construction of a shuttle clon (73) Assignee: Yeda Research and Development Co. ing vector. Applied Environmental Microbiology 72:527-535. Ltd., Rehovot (IL) EMBL: ACD97784.1. Alignment Only Being Sent.* Chenoll et al. 2012; Safety assessment of strain Bifidobacterium (*) Notice: Subject to any disclaimer, the term of this longum CECT 7347, a probiotic able to reduce the toxicity and patent is extended or adjusted under 35 inflammatory potential of gliadin-derived peptides, based on pheno U.S.C. 154(b) by 0 days. typic traits, whole genome sequencing, and murine trials. EMBL: CCK35109.18 (21) Appl. No.: 14/140,793 PajonEMBL et al. Clife2010; The genome sequenceC of Bifidobacterium longumgu Schell et al. 2002; The genome sequence of Bifidobacterium longum (22) Filed: Dec. 26, 2013 reflects its Apato the R gastrointestinal tract. SS (65) Prior Publication Data 12-1427 EMBL: AAN25255.1. Alignment Only Being US 2014/O178353 A1 Jun. 26, 2014 Wardetal. 2010; The genome sequence of Bifidobacterium sp. Strain 12 1 47BFAA) EMBL: EFV37145.1.* Related U.S. Application Data DeBoy et al. 2008; Insights into plant cell wall degradation from the genome sequence of soil bacterium Cellvibrio japonicas. J. Bacteri (60) Provisional application No. 61/745,838, filed on Dec. ology. 190: 5455-5463. EMBL: ACE841 12.1. Alighnment Only 26, 2012. Being Sent.* s Larimaretal. 2006; Annotation of the draft genome assembly of delta (51) Int. Cl. proteobacterium MLMS-1, EMBL: EAT06598.* Score Search Results; Percent Identity Comparison of SEQ ID No. Yite 3.08: 3001 with 45 other 793 sequences. 3. p Q Score Search Results; Percent Identity Comparison of SEQ ID No. CI2N 9/12 (2006.01) 2773 with 45 other 793 sequences. 2015.* C07K I4/8 (2006.01) Makarova et al. “Defense Islands in Bacterial and Archaeal Genomes A61 K38/00 (2006.01) and Prediction of Novel Defense Systems”, Journal of Bacteriology, (52) U.S. Cl. 193(21):6039-6056, Nov. 2011. CPC .............. CI2N 9/22 (2013.01); C07K 14/8107 (2013.01); CI2N 9/1241 (2013.01); A61K * cited by examiner 38/00 (2013.01) (58) Field of Classification Search Primary Examiner — Karen Cochrane Carlson CPC ....................................................... CO7K 14/OO See application file for complete search history. (57) ABSTRACT An isolated polypeptide is disclosed comprising an amino (56) References Cited acid sequence selected from the group consisting of SEQID NOS: 2773-5544 and 11089-11094, wherein the polypeptide U.S. PATENT DOCUMENTS has antimicrobial activity. Uses thereof for treating microbial infections are also disclosed. 5,994,118 A 11/1999 Moineau et al. 7,169,911 B2 1/2007 Durmaz et al. 7.550,576 B2 6/2009 Klaenhammer et al. 10 Claims, 13 Drawing Sheets 7,754,868 B2 7/2010 Klaenhammer et al. (10 of 13 Drawing Sheet(s) Filed in Color) U.S. Patent US 9,353,359 B2 U.S. Patent May 31 9 2016 Sheet 2 of 13 US 9,353,359 B2 (seuopuolinusº)4 U.S. Patent May 31, 2016 Sheet 3 of 13 US 9,353,359 B2 89'943 s s U.S. Patent May 31, 2016 Sheet 4 of 13 US 9,353,359 B2 sorar tific U.S. Patent May 31, 2016 Sheet 5 of 13 US 9,353,359 B2 3#8888 §§§§§§§§ U.S. Patent May 31, 2016 Sheet 6 of 13 US 9,353,359 B2 esou?ândøeseuotuopnasa? U.S. Patent May 31, 2016 Sheet 7 of 13 US 9,353,359 B2 Geo@ U.S. Patent May 31, 2016 Sheet 8 of 13 US 9,353,359 B2 **********x*{&#x23. ********@*$$ U.S. Patent May 31, 2016 Sheet 9 of 13 US 9,353,359 B2 U.S. Patent May 31, 2016 Sheet 10 of 13 US 9,353,359 B2 8 8 ''''''''''''''' 8x8x 838 era is x, 3e U.S. Patent May 31, 2016 Sheet 11 of 13 US 9,353,359 B2 &#3 90 Suojelus go equirM U.S. Patent US 9,353,359 B2 U.S. Patent May 31, 2016 Sheet 13 of 13 US 9,353,359 B2 o a o E co g s ba na C. c S. a. 8 ceog s S ca 5 E w wt is 3 es - E o t c c\ s d o 3 & a 2 to S 3 3 S 8 & 9 See eo) is OA. A Seuse, eo ui O A US 9,353,359 B2 1. 2 BACTERIAL ANT-PHAGE DEFENSE prokaryotic genomes (Shao et al., 2011). These systems (also SYSTEMS called TA modules), composed of a toxic gene and a neutral izing gene, were first suggested to function as plasmid addic RELATED APPLICATION tion molecules (Van Melderen and Saavedra De Bast, 2009: Wozniak and Waldor, 2009), but their prevalent existence on This application claims the benefit of priority under 35 chromosomes (Aizenman et al., 1996: Makarova et al., 2009: USC S 119(e) of U.S. Provisional Patent Application No. Shao et al., 2011) has led to the understanding that this is 61/745,838 filed Dec. 26, 2012, the contents of which are unlikely their major role. Accumulating evidence Suggest that incorporated herein by reference in their entirety. TA modules play pivotal roles in prokaryotic cellular biology 10 including programmed cell death (Hazan et al., 2004), stress GOVERNMENT INTERESTS response (Christensen et al., 2001), generation of persister cells (Schumacher et al., 2009), biofilm formation (Kimetal. Federally Sponsored Research 2009) and phage defense via abortive infection (Fineranet al., 15 2009; Hazan and Engelberg-Kulka, 2004: Koga et al., 2011; This invention was made with government Support under Pecota and Wood, 1996). AI082376 awarded by NIH. The government has certain The most prevalent kind of TA systems is type II systems, rights in the invention. where both toxin and antitoxin are proteins (as opposed to SEQUENCE LISTING STATEMENT types I and III where the antitoxin is a non-coding RNA (Fineran et al., 2009; Fozo et al.)). The two genes, which The ASCII file, entitled 57892SequenceListing..txt, created reside on the same operon, code for Small proteins and inhi on Nov. 11, 2013, comprising 20.497.456 bytes, submitted bition of the toxin is carried out through protein-protein inter concurrently with the filing of this application is incorporated action. As a rule, the toxin is a stable protein and the antitoxin herein by reference. is unstable and degrades rapidly by one of the housekeeping 25 bacterial proteases, usually Lon or Clplp (Aizenman et al., FIELD AND BACKGROUND OF THE 1996; Cherny and Gazit, 2004; Christensen et al., 2004; INVENTION Christensen et al., 2001; Christensen et al., 2003; Lehnherr and Yarmolinsky, 1995; Roberts et al., 1994; Van Melderenet The present invention, in some embodiments thereof, al., 1996). As a result, continuous production of the antitoxin relates to bacterial polypeptides that comprise toxin or anti 30 is required to prevent the toxins deleterious effects (Van toxin activity and, more particularly, but not exclusively, to Melderen and Saavedra De Bast, 2009). toxin-antitoxin pairs that may be used as bacterial anti-phage A number of reports demonstrate a role for type II TA defense systems. systems in phage resistance via an Abi mechanism: the exten Abroad array of food products, commodity chemicals, and sively studied MazEF system was shown to eliminate P1 biotechnology products are manufactured industrially by 35 phage infection (Hazan and Engelberg-Kulka, 2004), and the large-scale bacterial fermentation of various Substrates. recently identified RnlA toxin which is activated following Because enormous amounts of bacteria are being cultivated T4 phage infection degrades phage mRNAS (Koga et al., each day in large fermentation vats, bacteriophage contami 2011). Type I and Type IIITA systems (hok/sokand ToxIN, to nation can rapidly bring fermentations to a halt and cause respectively) were also shown to provide resistance against economic setbacks, and is therefore considered a serious 40 phages (Fineran et al., 2009; Pecota and Wood, 1996). How threat in these industries. The dairy fermentation industry has ever, based on their presence in bacterial defense islands, it openly acknowledged the problem of phage and has been was hypothesized that TA systems play a much wider role in working with academia and starter culture companies to phage defense (Makarova et al., 2011). develop defense strategies and systems to curtail the propa The usage of Abi Systems for biotech purposes, especially gation and evolution of phages for decades. 45 in protecting dairy industry bacteria from bacteriophages is To Survive in the face of perpetual phage attacks, bacteria disclosed in U.S. Pat. Nos. 7,754,868, 7,550,576, 7,169,911 have developed a variety of anti-phage defense systems (Lab and 5,994,118. rie et al., 2010; Sternand Sorek, 2011). These systems include To date, at least 12 families oftype IITA systems have been restriction enzymes that recognize and cleave foreign DNA described (Masuda et al., 2012; Shao et al., 2011). Members (King and Murray, 1994), abortive infection (Abi) mecha 50 of these families are widespread in bacterial and archaeal nisms that lead the bacterial cell, upon phage invasion, to genomes and undergo extensive horizontal gene transfer commit "suicide, thus protecting the colony against phage (Guglielmini et al., 2008: Makarova et al., 2009; Pandey and spread (Chopinet al., 2005); and the recently identified adap Gerdes, 2005: Shao et al., 2011).
Load more

Recommended publications
  • Recombinant E. Coli Lon Protease (C-6His)
    9853 Pacific Heights Blvd. Suite D. San Diego, CA 92121, USA Tel: 858-263-4982 Email: [email protected] 32-7101: Recombinant E. coli Lon Protease (C-6His) Gene : lon Gene ID : 945085 Uniprot ID : P0A9M0 Description Source: E.coli. MW :88.6kD. Recombinant E.coli Lon Protease is produced by our E.coli expression system and the target gene encoding Asn2-Lys784 is expressed with a 6His tag at the C-terminus. Lon Protease, is a member of the Lon protease family. They are found in archaea, bacteria and eukaryotes. Lon protease is ATP-dependent serine protease that mediates the selective degradation of mutant and abnormal proteins as well as certain short-lived regulatory proteins, including some antitoxins. It required for cellular homeostasis and for survival from DNA damage and developmental changes induced by stress. It degrades polypeptides processively to yield small peptide fragments that are 5 to 10 amino acids long and binds to DNA in a double-stranded, site- specific manner. Endogenous substrates include the regulatory proteins RcsA and SulA, the transcriptional activator SoxS, and UmuD. Its overproduction specifically inhibits translation through at least two different pathways, one of them being the YoeB- YefM toxin-antitoxin system. Product Info Amount : 10 µg / 50 µg Content : Supplied as a 0.2 µm filtered solution of 50mM TrisHCl, 100mM KCl, 10% Glycerol, pH 7.5 . Storage condition : Store at -20°C, stable for 6 months after receipt. Please minimize freeze-thaw cycles. Amino Acid : MGNPERSERIEIPVLPLRDVVVYPHMVIPLFVGREKSIRCLEAAMDHDKKIMLVAQKEASTDEPGVN
    [Show full text]
  • (12) Patent Application Publication (10) Pub. No.: US 2006/0110747 A1 Ramseier Et Al
    US 200601 10747A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2006/0110747 A1 Ramseier et al. (43) Pub. Date: May 25, 2006 (54) PROCESS FOR IMPROVED PROTEIN (60) Provisional application No. 60/591489, filed on Jul. EXPRESSION BY STRAIN ENGINEERING 26, 2004. (75) Inventors: Thomas M. Ramseier, Poway, CA Publication Classification (US); Hongfan Jin, San Diego, CA (51) Int. Cl. (US); Charles H. Squires, Poway, CA CI2O I/68 (2006.01) (US) GOIN 33/53 (2006.01) CI2N 15/74 (2006.01) Correspondence Address: (52) U.S. Cl. ................................ 435/6: 435/7.1; 435/471 KING & SPALDING LLP 118O PEACHTREE STREET (57) ABSTRACT ATLANTA, GA 30309 (US) This invention is a process for improving the production levels of recombinant proteins or peptides or improving the (73) Assignee: Dow Global Technologies Inc., Midland, level of active recombinant proteins or peptides expressed in MI (US) host cells. The invention is a process of comparing two genetic profiles of a cell that expresses a recombinant (21) Appl. No.: 11/189,375 protein and modifying the cell to change the expression of a gene product that is upregulated in response to the recom (22) Filed: Jul. 26, 2005 binant protein expression. The process can improve protein production or can improve protein quality, for example, by Related U.S. Application Data increasing solubility of a recombinant protein. Patent Application Publication May 25, 2006 Sheet 1 of 15 US 2006/0110747 A1 Figure 1 09 010909070£020\,0 10°0 Patent Application Publication May 25, 2006 Sheet 2 of 15 US 2006/0110747 A1 Figure 2 Ester sers Custer || || || || || HH-I-H 1 H4 s a cisiers TT closers | | | | | | Ya S T RXFO 1961.
    [Show full text]
  • Online Proofing
    elsevier_BBABIO_47641 Emerging role of Lon protease as a master regulator of mitochondrial functions Marcello Pintia, 1 Lara Gibellinib, 1 Milena Nasib Sara De Biasib Carlo Augusto Bortolottia Anna Iannonec Andrea Cossarizzab, ⁎ [email protected] aDepartment of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy bDepartment of Surgery, Medicine, Dentistry and Morphological Sciences, University of Modena and Reggio Emilia, Modena, Italy cDepartment of Diagnostics, Clinical and Public Health Medicine, University of Modena and Reggio Emilia, Modena, Italy ⁎Corresponding author at: Department of Surgery, Medicine, Dentistry, and Morphological Sciences, University of Modena and Reggio Emilia, Via Campi, 287, 41125 Modena, Italy. 1Equally contributed to the paper. This article is part of a Special Issue entitled '‘EBEC 2016: 19th European Bioenergetics Conference, Riva del Garda, Italy, July 2‐–6, 2016'’, edited by Prof. Paolo Bernardi. Abstract Lon protease is a nuclear-encoded, mitochondrial ATP-dependent protease highly conserved throughout the evolution, crucial for the maintenance of mitochondrial homeostasis. Lon acts as a chaperone of misfolded proteins, and is necessary for maintaining mitochondrial DNA. The impairment of these functions has a deep impact on mitochondrial functionality and morphology. An altered expression of Lon leads to a profound reprogramming of cell metabolism, with a switch from respiration to glycolysis, which is often observed in cancer cells. Mutations of Lon, which likely impair its chaperone properties, are at the basis of a genetic inherited disease named of the cerebral, ocular, dental, auricular, skeletal (CODAS) syndrome. This article is part of a Special Issue entitled '‘EBEC 2016: 19th European Bioenergetics Conference, Riva del Garda, Italy, July 2‐–6, 2016'’, edited by Prof.
    [Show full text]
  • Sarah Owdah Alomrani.Pdf
    Expression of the rice cystatin, Oryzacystatin-I (OC-I) influences the plant growth and development Sarah Owdah Alomrani Submitted in accordance with the requirements for the degree of Doctor of Philosophy The University of Leeds Faculty of Biological Sciences Centre for Plant Sciences September 2020 i The candidate confirms that the work submitted is his/her own and that appropriate credit has been given where reference has been made to the work of others. This copy has been supplied on the understanding that it is copyright material and that no quotation from the thesis may be published without proper acknowledgement. © 2020, The University of Leeds, Sarah Alomrani ii Acknowledgment Today, I have completed the writing of my thesis during the lockdown period which has been enforced due to the COVID-19 pandemic. Before I thank those who have support me through my journey, I would like to mention that, when I got divorced, around five years ago, I felt broken and I will always remember that my father told me: “You can start on your next chapter as an independent Saudi women”. I thought that the only thing that people will know about me was that I had been divorced, but now that is not the case. I have worked hard to obtain a scholarship to study in UK in my favourite subject, plant sciences, and the most important thing about me now is that I’m a strong women who no longer hopes for someone who would bring flowers for her, but I am able to plant my own flowers.
    [Show full text]
  • Emerging Role of Lon Protease As a Master Regulator of Mitochondrial Functions☆
    Biochimica et Biophysica Acta 1857 (2016) 1300–1306 Contents lists available at ScienceDirect Biochimica et Biophysica Acta journal homepage: www.elsevier.com/locate/bbabio Emerging role of Lon protease as a master regulator of mitochondrial functions☆ Marcello Pinti a,1, Lara Gibellini b,1,MilenaNasib,SaraDeBiasib,CarloAugustoBortolottia, Anna Iannone c, Andrea Cossarizza b,⁎ a Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy b Department of Surgery, Medicine, Dentistry and Morphological Sciences, University of Modena and Reggio Emilia, Modena, Italy c Department of Diagnostics, Clinical and Public Health Medicine, University of Modena and Reggio Emilia, Modena, Italy article info abstract Article history: Lon protease is a nuclear-encoded, mitochondrial ATP-dependent protease highly conserved throughout the evo- Received 13 January 2016 lution, crucial for the maintenance of mitochondrial homeostasis. Lon acts as a chaperone of misfolded proteins, Received in revised form 23 March 2016 and is necessary for maintaining mitochondrial DNA. The impairment of these functions has a deep impact on mi- Accepted 24 March 2016 tochondrial functionality and morphology. An altered expression of Lon leads to a profound reprogramming of Available online 28 March 2016 cell metabolism, with a switch from respiration to glycolysis, which is often observed in cancer cells. Mutations of Lon, which likely impair its chaperone properties, are at the basis of a genetic inherited disease named of Keywords: Lon the cerebral, ocular, dental, auricular, skeletal (CODAS) syndrome. This article is part of a Special Issue entitled Protease ‘EBEC 2016: 19th European Bioenergetics Conference, Riva del Garda, Italy, July 2–6, 2016’,editedbyProf.
    [Show full text]
  • PDZ Domains in Microorganisms: Link Between Stress Response 2 and Protein Synthesis
    bioRxiv preprint doi: https://doi.org/10.1101/186510; this version posted September 10, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 PDZ Domains in Microorganisms: Link between Stress Response 2 and Protein Synthesis 3 Vijaykumar Yogesh Muley1, 2, * and Sanjeev Galande1,* 4 1 Centre of Excellence in Epigenetics, Indian Institute of Science Education and Research, 5 Pune, Maharashtra, 411 008, India 6 2 Present Address - Gut Inflammation Group, APC Microbiome Institute, University College 7 Cork, Cork, Ireland 8 * To whom correspondence should be addressed. 9 E mail: SG: [email protected]; VYM: [email protected] 10 11 Abstract The PSD-95/Dlg-A/ZO-1 (PDZ) domain is highly expanded and diversified in 12 metazoan where it is known to assemble diverse signalling components by virtue of interactions 13 with other proteins in sequence-specific manner. In contrast, in bacteria it monitors protein 14 quality control during stress response. The distribution, functions and origin of PDZ domain- 15 containing proteins in prokaryotes are largely unknown. We analyzed 7,852 PDZ domain- 16 containing proteins in 1,474 prokaryotes and fungi. PDZ domains are abundant in eubacteria; 17 and, this study confirms their occurrence also in archaea and fungi. Of all eubacterial PDZ 18 domain-containing proteins, 89% are predicted to be membrane and periplasmic, explaining the 19 depletion of bacterial domain forms in metazoan.
    [Show full text]
  • BMC Genomics Biomed Central
    BMC Genomics BioMed Central Research article Open Access Cross genome comparisons of serine proteases in Arabidopsis and rice Lokesh P Tripathi and R Sowdhamini* Address: National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bellary Road, Bangalore 560 065, India Email: Lokesh P Tripathi - [email protected]; R Sowdhamini* - [email protected] * Corresponding author Published: 09 August 2006 Received: 11 April 2006 Accepted: 09 August 2006 BMC Genomics 2006, 7:200 doi:10.1186/1471-2164-7-200 This article is available from: http://www.biomedcentral.com/1471-2164/7/200 © 2006 Tripathi and Sowdhamini; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Serine proteases are one of the largest groups of proteolytic enzymes found across all kingdoms of life and are associated with several essential physiological pathways. The availability of Arabidopsis thaliana and rice (Oryza sativa) genome sequences has permitted the identification and comparison of the repertoire of serine protease-like proteins in the two plant species. Results: Despite the differences in genome sizes between Arabidopsis and rice, we identified a very similar number of serine protease-like proteins in the two plant species (206 and 222, respectively). Nearly 40% of the above sequences were identified as potential orthologues. Atypical members could be identified in the plant genomes for Deg, Clp, Lon, rhomboid proteases and species-specific members were observed for the highly populated subtilisin and serine carboxypeptidase families suggesting multiple lateral gene transfers.
    [Show full text]
  • Role of the AAA Protease Yme1 in Folding of Proteins in the Mitochondrial Intermembrane Space
    Role of the AAA protease Yme1 in folding of proteins in the mitochondrial intermembrane space Bernadette Schreiner München 2012 Role of the AAA protease Yme1 in folding of proteins in the mitochondrial intermembrane space Dissertation zur Erlangung des Doktorgrades der Fakultät für Biologie der Ludwig-Maximilians-Universität München vorgelegt von Bernadette Schreiner aus Limburgerhof München 2012 Eidesstattliche Erklärung Ich versichere hiermit an Eides statt, dass die vorgelegte Dissertation von mir selbständig und ohne unerlaubte Hilfe angefertigt ist. München, den 31. 01. 2013 Bernadette Schreiner Dissertation eingereicht am: 11. 12. 2012 Tag der mündlichen Prüfung: 29. 01. 2013 Erstgutachter: Prof. Dr. Jürgen Soll Zweitgutachter: Prof. Dr. Ute Vothknecht Sondergutachter: Prof. Dr. Dr. Walter Neupert Für meine Familie INTRODUCTION TABLE OF CONTENTS 1. INTRODUCTION ................................................................................................7 1.1 Cellular protein quality control systems ...............................................................7 1.1.1 Proteins - the worker molecules of the cell ........................................................7 1.1.2 Protein quality control and homeostasis (proteostasis) ......................................8 1.1.3 Failure of protein quality control and homeostasis ............................................9 1.2 Molecular chaperones .............................................................................................9 1.2.1 The Hsp70 system ............................................................................................10
    [Show full text]
  • Deletion of Heat Shock Protein 60 in Adult Mouse Cardiomyocytes Perturbs Mitochondrial Protein Homeostasis and Causes Heart Failure
    Cell Death & Differentiation (2020) 27:587–600 https://doi.org/10.1038/s41418-019-0374-x ARTICLE Deletion of heat shock protein 60 in adult mouse cardiomyocytes perturbs mitochondrial protein homeostasis and causes heart failure 1 1 1 2 1 3 1 1 Feifei Fan ● Yaoyun Duan ● Feili Yang ● Christa Trexler ● Hong Wang ● Lei Huang ● Yali Li ● Huayuan Tang ● 4 2 4 5 2 1 Gang Wang ● Xi Fang ● Jie Liu ● Nan Jia ● Ju Chen ● Kunfu Ouyang Received: 12 March 2019 / Revised: 10 May 2019 / Accepted: 5 June 2019 / Published online: 17 June 2019 © The Author(s) 2019. This article is published with open access Abstract To maintain healthy mitochondrial enzyme content and function, mitochondria possess a complex protein quality control system, which is composed of different endogenous sets of chaperones and proteases. Heat shock protein 60 (HSP60) is one of these mitochondrial molecular chaperones and has been proposed to play a pivotal role in the regulation of protein folding and the prevention of protein aggregation. However, the physiological function of HSP60 in mammalian tissues is not fully understood. Here we generated an inducible cardiac-specific HSP60 knockout mouse model, and demonstrated that HSP60 deletion in adult mouse hearts altered mitochondrial complex activity, mitochondrial membrane potential, and ROS production, and eventually led to dilated cardiomyopathy, heart failure, and lethality. Proteomic analysis was performed in purified control and mutant mitochondria before mutant hearts developed obvious cardiac abnormalities, and revealed a list of mitochondrial-localized proteins that rely on HSP60 (HSP60-dependent) for correctly folding in mitochondria. We also utilized an in vitro system to assess the effects of HSP60 deletion on mitochondrial protein import and protein stability after import, and found that both HSP60-dependent and HSP60-independent mitochondrial proteins could be normally imported in mutant mitochondria.
    [Show full text]
  • Genome-Wide Survey of Prokaryotic Serine Proteases: Analysis Of
    BMC Genomics BioMed Central Research article Open Access Genome-wide survey of prokaryotic serine proteases: Analysis of distribution and domain architectures of five serine protease families in prokaryotes Lokesh P Tripathi1,2 and R Sowdhamini*1 Address: 1National Centre for Biological Sciences, TIFR, GKVK Campus, Bellary Road, Bangalore-560065, India and 2Current address: National Institute of Biomedical Innovation, 7-6-8 Asagi Saito Ibaraki-City, Osaka, 567-0085, Japan Email: Lokesh P Tripathi - [email protected]; R Sowdhamini* - [email protected] * Corresponding author Published: 19 November 2008 Received: 23 February 2008 Accepted: 19 November 2008 BMC Genomics 2008, 9:549 doi:10.1186/1471-2164-9-549 This article is available from: http://www.biomedcentral.com/1471-2164/9/549 © 2008 Tripathi and Sowdhamini; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Serine proteases are one of the most abundant groups of proteolytic enzymes found in all the kingdoms of life. While studies have established significant roles for many prokaryotic serine proteases in several physiological processes, such as those associated with metabolism, cell signalling, defense response and development, functional associations for a large number of prokaryotic serine proteases are relatively unknown. Current analysis is aimed at understanding the distribution and probable biological functions of the select serine proteases encoded in representative prokaryotic organisms. Results: A total of 966 putative serine proteases, belonging to five families, were identified in the 91 prokaryotic genomes using various sensitive sequence search techniques.
    [Show full text]
  • Nirmala Padmanabhan-Phd Thesis
    The Saccharomyces cerevisiae HtrA orthologue, Ynm3, is a chaperone-protease that aids survival under heat stress PhD Thesis in partial fulfilment of the requirements for the degree “Doctor of Philosophy” in the Molecular Biology Program at the Georg August University Göttingen, Faculty of Biology submitted by Nirmala Padmanabhan born in Trivandrum, India 2008 I hereby declare that the PhD thesis entitled “The Saccharomyces cerevisiae HtrA orthologue, Ynm3, is a chaperone-protease that aids survival under heat stress” has been written independently and with no other sources and aids than quoted. Nirmala Padmanabhan i To my grandfather, Late Mr. P. Rama Iyer ii Acknowledgements Acknowledgements This work was performed in the Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Georg August University, Goettingen. I am grateful to my mentor and supervisor Prof. Gerhard H. Braus for giving me the opportunity to pursue my PhD work in his laboratory and for his constant encouragement and support. I am thankful to Dr. Lars Fichtner for his involvement in my work and for his friendly support throughout my PhD. My doctoral committee members, Prof. Christiane Gatz and Prof. Jörg B. Schulz have given me their time and support, for which I am thankful. Prof. Schulz was involved in my work from the very beginning and has invited me to regularly present my work in his departmental seminars. I am beholden to the following people for their help and collaborations, without which this work would not be in its present form. Ms. Maria Meyer for the vast amount of technical assistance and for organizing the activities of Lab 107, which made working easier.
    [Show full text]
  • Supercomputing in Science and Engineering
    SUPERCOMPUTING IN SCIENCE AND ENGINEERING IT4Innovations National Supercomputing Center Czech Republic 2017 nova_verze.indd 1 03.04.2017 15:16:08 VŠB – Technical University of Ostrava Supercomputing in Science and Engineering Editors: Karina Pešatová, Barbora Poláková, John Cawley Ostrava, 2017 Published by VŠB – Technical University of Ostrava Design and typesetting: Milan Smetana, Emílie Smetanová Page count: 224 Edition: 1st Printed by: Knowlimits, s.r.o. Copies: 300 Not for sale © IT4Innovations National Supercomputing Center This work is subject to copyright. All rights reserved. Reproduction or publication of this material, even partial, is allowed only with the editors’ permission. ISBN 978-80-248-4037-6 2 nova_verze.indd 2 03.04.2017 15:16:08 SUPERCOMPUTING IN SCIENCE AND ENGINEERING IT4Innovations National Supercomputing Center Czech Republic 2017 Editors: Karina Pešatová, Barbora Poláková, John Cawley Reviewers: Martin Palkovič, Branislav Jansík, Vít Vondrák, Tomáš Kozubek, Jan Martinovič, René Kalus, Tomáš Brzobohatý This publication was supported by The Ministry of Education, Youth and Sports from the Large Infrastructures for Research, Experimental Development and Innovations project „IT4Innovations National Supercomputing Center – LM2015070“ 3 nova_verze.indd 3 03.04.2017 23:20:09 Table of contents Director’s introduction 9 Martin Palkovič The infrastructure of IT4Innovations 10 01 ASTROPHYSICS Computational Planetology: Timing of Water Plume Eruptions on Enceladus Explained 16 by Interior Viscosity Structure Marie Běhounková
    [Show full text]