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Functional Analysis of Peptidases from the Cyanobacterium Synechocystis

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Functional analysis of peptidases from the cyanobacterium Synechocystis sp. PCC 6803 Dissertation zur Erlangung des Doktorgrades der Fakultät für Biologie der Ludwig-Maximilians-Universität München vorgelegt von Elena Pojidaeva aus Moskau, Russland München 30.Juni 2004 1. Gutachter: Prof. Dr. R. G. Herrmann 2. Gutachter: Prof. Dr. H. Scheer Tag der mündlichen Prüfung: 16.09.2004 To my family CONTENT I CONTENT Abbreviations ……………………………………………………………………………………… V 1. INTRODUCTION ……………………………………………………………………………. 1 1.1 Proteolytic enzymes and their role in cell homeostasis ………………….………... 1 1.2 Characterization of the protease complement of cyanobacterial cells ……….. 7 1.2.1 The Clp peptidase family ………………………………………………………………. 8 1.2.2 The Deg peptidase family …………………………………………………………….… 9 1.2.3 The FtsH peptidase family ……………………………………………………………… 10 1.2.4 The Ctp family of carboxypeptidases …………………………………………………... 11 1.2.5 The SppA peptidase family ……………………………………………………………… 12 1.3 Cyanobacteria as models for the analysis of the photosynthetic machinery … 13 1.3.1 Structure of cyanobacterial photosynthetic complexes …………………………………. 13 1.3.2 Adaptation of cyanobacteria to environmental changes ………………………………… 17 1.3.2.1 Light acclimation …………………………………………………………….. 17 1.3.2.2 Heat stress ……………………………………………………………………. 19 1.3.2.3 Nutrient stress ……………………………………….……………………….. 20 2. MATERIALS AND METHODS ………………………………………..…………………. 22 2.1 Materials …………………………………………………………………………..……………. 22 2.1.1 Chemicals and enzymes …………………………………………………………………. 22 2.1.2 Molecular weight markers ……………………………………………………………….. 22 2.1.3 Vectors and strains ………………………………………………………………………. 23 2.1.4 Antibodies ……………………………………………………………………………….. 23 2.1.5 Oligonucleotides ………………………………………………………………………… 23 2.1.5.1 Primers for Escherichia coli strains …………………………………………... 24 2.1.5.2 Synechocystis gene-specific primers ………………………….………………. 24 2.1.6 General buffers and solutions ……………………………………………………………. 25 2.1.7 Medium for bacterial growth …………………………………………….. ……………… 26 2.1.8 Transfer membranes ……………………………………………………………………… 27 2.1.9 Plant material …………………………………………………………………………….. 28 2.2 Methods ……………………………………………………………………………………..…… 28 2.2.1 Sequence analysis ………………………………………………………………………… 28 2.2.2 Strains and growth conditions for Synechocystis ………………………………………… 28 2.2.3 Construction of knock-out mutants in Synechocystis ……………………………..……. 29 2.2.3.1 Construction of recombinant plasmids ………………………………………. 29 CONTENT II 2.2.3.2 Transformation of Synechocystis …………………………………………….. 30 2.2.3.3 Conjugal transfer of plasmids into cyanobacterial cells ……….…………….. 31 2.2.4 DNA and RNA analysis …………………………………………………………………. 31 2.2.4.1 DNA isolation from Synechocystis …………………………………………… 31 2.2.4.2 PCR analysis …………………………………………………………………. 32 2.2.4.3 Isolation of plasmid DNA from E. coli ………………………………………. 32 2.2.4.4 RNA isolation from Synechocystis ………………………..…………………. 32 2.2.4.5 Analysis of gene expression …….……………………………………………. 33 2.2.4.5.1 Northern analysis …………………………………………………. 33 2.2.4.5.2 RT-PCR …………………………………………………………… 34 2.2.5 Overexpression of proteins ………………………………………………………………. 34 2.2.5.1 Overexpression of proteins in E. coli cells …………………….……………… 34 2.2.5.2 Overexpression of proteins in E. coli lysates ………………….……………… 35 2.2.6 Generation of protein-specific antisera ……………………………..…………………….. 35 2.2.6.1 Preparation of probes for rabbit immunization ……………………………….. 35 2.2.6.2. Injection of rabbits and antibody preparation ……………….……………….. 35 2.2.6.3 Purification of antibodies ………..……………………………………………. 36 2.2.6.3.1 Purification of antibodies with overexpressed protein on the membrane …………………………………………… 36 2.2.9.3.2 Purification of antibodies with Protein A-Sepharose ………..……………………………….. 36 2.2.7 Pigment analysis of Synechocystis cells ………………………………………………….. 37 2.2.7.1 Determination of chlorophyll a concentration ………………………………... 37 2.2.7.2 Determination of carotenoid concentration …………………………………… 37 2.2.7.3 Determination of C-phycocyanin concentration ……………….……………… 37 2.2.8 Determination of cell densities …………………………………………………………… 38 2.2.9 Protein analysis …………………………………………………………………………… 38 2.2.9.1 Determination of protein concentrations ……………………….…………….. 38 2.2.9.2 Protein gel electrophoresis ……………………………………………………. 39 2.2.9.2.1 Gel electrophoresis according to Laemmli (1970) ….…………….. 39 2.2.8.2.2 Gel electrophoresis according to Kashino (2001) ……...........……. 39 2.2.9.3 Staining of PAA gels ………………………………………………………….. 40 2.2.9.3.1 Coomassie Brilliant Blue staining ………………….……………… 40 2.2.9.3.2. Silver staining ……………………………………….……………. 41 2.2.9.3.3. Imidazol staining ………………………………………………….. 42 2.2.9.4 Isolation and fractionation of thylakoid membranes…………………………… 42 2.2.9.4.1 Isolation of total cellular and membrane proteins from Synechocystis ………………………………………………… 42 2.2.9.4.2 Extraction of peripherally associated proteins …………………….. 43 2.2.9.4.3 Preparation of phycobilisomes …………………………………….. 43 2.2.9.4.4 Isolation of photosynthetic complexes from Synechocystis cells by sucrose gradient centrifugation ……………..……………... 44 2.2.9.4.5 Isolation of photosynthetic complexes from Synechocystis by non-denaturing gel electrophoresis ……………………………… 44 2.2.9.5 Immunological detection of proteins …..……………………………………… 46 2.2.9.5.1 Transfer of proteins onto nitrocellulose membranes ………………. 46 CONTENT III 2.2.9.5.2 Staining blots with Ponceau S ……………………………………. 47 2.2.9.5.3 Western analysis using horseradish peroxidase-conjgated antibodies ………………………………….. 47 2.2.9.5.4 Western analysis using I125 labeled Protein A antibody …………. 48 2.2.10 Proteolysis assay ………………….………………….………………………………… 48 2.2.11 Protein pulse-labeling with 35S-methionine …………………………………………… 49 2.2.12 Measurements of oxygen evolution by the Clark electrode ………………………………. 49 2.2.13 Low temperature (77K) fluorescence analysis …………………………………..……. 49 3. RESULTS ………………………………………………………………………………..……… 51 3.1 Characterization of peptidases in Synechocystis …………………………………………….…. 51 3.1.1 Physiological analysis of peptidase knock-out mutant strains ……………………….… 52 3.1.1.1 Acclimation of cyanobacterial cells to different light intensities ………….… 53 3.1.1.2 Heat stress ………………………………………………………………….… 53 3.1.1.3 Nutrient deprivation ................................................................................……. 55 3.2 Functional analysis of the SppA peptidase family in Synechocystis ……………………………. 57 3.2.1 Functional analysis of SppA1 protease ……………………………………………….…. 57 3.2.1.1 Analysis of SppA1 protein sequence ………………………………………. 57 3.2.1.2 Construction of ∆sppA1 and complement pVZsppA1 mutant strains……….. 59 3.2.1.3 Analysis of sppA1 gene …………………………………………………….. 61 3.2.1.4 Expression of the sppA1 gene under different light intensities ……….……. 63 3.2.1.5 Phenotypical characterization of the ∆sppA1 ………………………………. 63 3.2.1.6 Spectroscopic characterization of the ∆sppA1 ……………………………… 67 3.2.1.7 Analysis of content of photosynthetic proteins …………………………….. 69 3.2.1.8 Genes and expression analysis of phycobiliproteins ……………………….. 70 3.2.1.9 In vivo labeling of the wild-type and ∆sppA1 ………………………………. 72 3.2.1.10 Kinetics of phycobiliproteins degradation ………………………………….. 73 3.2.1.11 Analysis of phycobiliproteins ……………………………………………….. 74 3.2.1.11.1 Characterization and isolation of phycobilisomes …………..………. 74 3.2.1.11.2 SppA1 is involved in the light-dependent cleavage of rod linkers ……………………………………………………….. 76 3.2.2 Functional analysis of SppA2 protease …………………………………………….……. 78 3.2.2.1 Analysis of SppA2 amino acid sequence ……………………………….……. 78 3.2.2.2 Overexpression of SppA2 protein …………………………………………… 79 3.2.2.3 Analysis of proteolytic activity of SppA2 …………………………………… 81 3.2.2.4 Localization of the SppA2 protein …………………………………………… 82 3.2.2.4.1 Intracellular localization of the SppA2 protein …………………… 82 3.2.2.4.2 Association of SppA2 protein with membrane structures ………… 82 3.2.2.4.3 Localization of SppA2 in a high molecular weight membrane complex ……………………………………….. 83 3.2.2.4.4 Isolation of photosynthetic complexes by non-denaturing “blue-native” PAGE ……………………………… 84 3.2.2.5 Expression analysis of SppA2 ……………………………………………….. 87 3.2.2.5.1 Expression of sppA2 gene during different light regimes ………… 87 3.2.2.5.2 SppA2 protein levels under various stress conditions ..………….. 88 3.2.2.5.3 Kinetics of SppA2 degradation upon HL exposure and its acclimation during recovery from HL to LL …… 89 3.2.2.6 Construction of sppA2-depleted and complemented mutant strains …………. 90 CONTENT IV 3.2.2.7 Phenotypical characterization of the ∆sppA2 mutant strain ………………….. 92 3.2.2.8 Analysis of protein synthesis in ∆sppA2 under LL and HL regimes …………. 93 3.2.2.9 Biochemical analysis of ∆sppA2 thylakoid proteins under LL and HL regimes ………………………………………………….. 94 3.2.2.10 Characterization of wild-type and ∆sppA2 strains after recovery conditions from HL to LL ……………………………………….. 96 3.2.2.10.1 Photosynthetic activity of cells under different light regimes ….. 96 3.2.2.10.2 Biochemical analysis of ∆sppA2 thylakoid proteins under LL and HL regimes …………………….. 97 4. DISCUSSION …………………………………………………………………………………….. 98 4.1 Comparison of the protease complement in cyanobacteria and the Arabidopsis chloroplast … 98 4.2 Role of peptidases in the adaptation of thylakoid membranes to environmental stress ……….. 106 4.2.1 Light stress ……………………………………………………………………………….. 107 4.2.2 Heat stress ………………………………………………………………………………… 107 4.2.3 Nutrient stress ..................................................................................................................... 108 4.3 The SppA protease family
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    USOO7608700B2 (12) United States Patent (10) Patent No.: US 7,608,700 B2 Klaenhammer et al. (45) Date of Patent: Oct. 27, 2009 (54) LACTOBACILLUS ACIDOPHILUS NUCLEIC WO WO 2004/069 178 A2 8, 2004 ACID SEQUENCES ENCODING WO WO 2004/096992 A2 11/2004 STRESS-RELATED PROTEINS AND USES WO WO 2005/001057 A2 1, 2005 THEREFOR WO WO 2005/O12491 A2 2, 2005 (75) Inventors: Todd R. Klaenhammer, Raleigh, NC (US); Eric Altermann, Apex. NC (US); OTHER PUBLICATIONS M. Andrea Azcarate-Peril, Raleigh, NC (US); Olivia McAuliffe, Cork (IE): W. Bowie et al (Science, 1990, 257: 1306-1310).* Michael Russell, Newburgh, IN (US) Journal of Molecular Microbiology and Biotechnology (2002), 4(6), 525-532), abstract only.* (73) Assignee: North Carolina State University, Boehringer Mannheim Biochemicals (1991 Catalog p. 557); Raleigh, NC (US) Stratagene (1991 Product Catalog, p. 66); Gibco BRL (Catalogue & Reference Guide 1992, p. 292).* (*) Notice: Subject to any disclaimer, the term of this Promega (1993/1994 Catalog, pp. 90-91); New England BioLabs patent is extended or adjusted under 35 (Catalog 1986/1987, pp. 60-62).* U.S.C. 154(b) by 262 days. Abee et al. (1994) “Kinetic studies of the action of lactacin F, a bacteriocin produced by Lactobacillus johnsonii that formsporation (21) Appl. No.: 11/074,176 complexes in the cytoplasmic membrane' Appl. Environ. Microbiol. 60:1006-1013. (22) Filed: Mar. 7, 2005 Allison and Klaenhammer (1996) “Functional analysis of the gene encoding immunity to lactacin F. lafl. and its use as a Lactobacillus (65) Prior Publication Data specific, food-grade genetic marker Appl.
  • Protein Maturation and Proteolysis in Plant Plastids, Mitochondria, and Peroxisomes

    Protein Maturation and Proteolysis in Plant Plastids, Mitochondria, and Peroxisomes

    PP66CH04-VanWijk ARI 30 March 2015 20:57 Protein Maturation and Proteolysis in Plant Plastids, Mitochondria, and Peroxisomes Klaas J. van Wijk Department of Plant Biology, Cornell University, Ithaca, New York 14853; email: [email protected] Annu. Rev. Plant Biol. 2015. 66:75–111 Keywords First published online as a Review in Advance on proteome remodeling, endosymbiotic organelle, degron, proteostasis, January 12, 2015 degradomics, autophagy The Annual Review of Plant Biology is online at plant.annualreviews.org Abstract This article’s doi: Plastids, mitochondria, and peroxisomes are key organelles with dynamic 10.1146/annurev-arplant-043014-115547 proteomes in photosynthetic eukaryotes. Their biogenesis and activity must Copyright c 2015 by Annual Reviews. be coordinated and require intraorganellar protein maturation, degradation, All rights reserved and recycling. The three organelles together are predicted to contain ∼200 Annu. Rev. Plant Biol. 2015.66:75-111. Downloaded from www.annualreviews.org presequence peptidases, proteases, aminopeptidases, and specific protease chaperones/adaptors, but the substrates and substrate selection mechanisms are poorly understood. Similarly, lifetime determinants of organellar pro- teins, such as N-end degrons and tagging systems, have not been identi- fied, but the substrate recognition mechanisms likely share similarities be- tween organelles. Novel degradomics tools for systematic analysis of protein lifetime and proteolysis could define such protease-substrate relationships, Access provided by Chinese Academy of Agricultural Sciences (Agricultural Information Institute) on 05/10/16. For personal use only. degrons, and protein lifetime. Intraorganellar proteolysis is complemented by autophagy of whole organelles or selected organellar content, as well as by cytosolic protein ubiquitination and degradation by the proteasome.