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Kavela S, Vyas P, CP J, Kushwaha SK, Majumdar SS, Faisal SM. Use of an Integrated Multi-Omics Approach To Identify Molecular Mechanisms and Critical Factors Involved in the Pathogenesis of Leptospira. Microbiol Spectr 2023; 11:e0313522. [PMID: 36853003 PMCID: PMC10100824 DOI: 10.1128/spectrum.03135-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 02/06/2023] [Indexed: 03/01/2023] Open
Abstract
Leptospirosis, a bacterial zoonosis caused by pathogenic Leptospira spp., is prevalent worldwide and has become a serious threat in recent years. Limited understanding of Leptospira pathogenesis and host response has hampered the development of effective vaccine and diagnostics. Although Leptospira is phagocytosed by innate immune cells, it resists its destruction, and the evading mechanism involved is unclear. In the present study, we used an integrative multi-omics approach to identify the critical molecular factors of Leptospira involved in pathogenesis during interaction with human macrophages. Transcriptomic and proteomic analyses were performed at 24 h postinfection of human macrophages (phorbol-12-myristate-13-acetate differentiated THP-1 cells) with the pathogenic Leptospira interrogans serovar Icterohaemorrhagiae strain RGA (LEPIRGA). Our results identified a total of 1,528 transcripts and 871 proteins that were significantly expressed with an adjusted P value of <0.05. The correlations between the transcriptomic and proteomic data were above average (r = 0.844), suggesting the role of the posttranscriptional processes during host interaction. The conjoint analysis revealed the expression of several virulence-associated proteins such as adhesins, invasins, and secretory and chemotaxis proteins that might be involved in various processes of attachment and invasion and as effectors during pathogenesis in the host. Further, the interaction of bacteria with the host cell (macrophages) was a major factor in the differential expression of these proteins. Finally, eight common differentially expressed RNA-protein pairs, predicted as virulent, outer membrane/extracellular proteins were validated by quantitative PCR. This is the first report using integrated multi-omics approach to identify critical factors involved in Leptospira pathogenesis. Validation of these critical factors may lead to the identification of target antigens for the development of improved diagnostics and vaccines against leptospirosis. IMPORTANCE Leptospirosis is a zoonotic disease of global importance. It is caused by a Gram-negative bacterial spirochete of the genus Leptospira. The current challenge is to detect the infection at early stage for treatment or to develop potent vaccines that can induce cross-protection against various pathogenic serovars. Understanding host-pathogen interactions is important to identify the critical factors involved in pathogenesis and host defense for developing improved vaccines and diagnostics. Utilizing an integrated multi-omics approach, our study provides important insight into the interaction of Leptospira with human macrophages and identifies a few critical factors (such as virulence-associated proteins) involved in pathogenesis. These factors can be exploited for the development of novel tools for the detection, treatment, or prevention of leptospirosis.
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Affiliation(s)
- Sridhar Kavela
- Laboratory of Vaccine Immunology, National Institute of Animal Biotechnology, Hyderabad, India
| | - Pallavi Vyas
- Laboratory of Vaccine Immunology, National Institute of Animal Biotechnology, Hyderabad, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Jusail CP
- Laboratory of Vaccine Immunology, National Institute of Animal Biotechnology, Hyderabad, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Sandeep K. Kushwaha
- Bioinformatics Lab, National Institute of Animal Biotechnology, Hyderabad, India
| | - Subeer S. Majumdar
- Gene and Protein Engineering Lab, National Institute of Animal Biotechnology, Hyderabad, India
| | - Syed M. Faisal
- Laboratory of Vaccine Immunology, National Institute of Animal Biotechnology, Hyderabad, India
- Regional Centre for Biotechnology, Faridabad, India
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cKMT1 is a new lysine methyltransferase that methylates the ferredoxin-NADP(+) oxidoreductase (FNR) and regulates energy transfer in cyanobacteria. Mol Cell Proteomics 2023; 22:100521. [PMID: 36858286 PMCID: PMC10090440 DOI: 10.1016/j.mcpro.2023.100521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 02/20/2023] [Accepted: 02/24/2023] [Indexed: 03/03/2023] Open
Abstract
Lysine methylation is a conserved and dynamic regulatory post-translational modification performed by lysine methyltransferases (KMTs). KMTs catalyze the transfer of mono-, di-, or tri-methyl groups to substrate proteins and play a critical regulatory role in all domains of life. To date, only one KMT has been identified in cyanobacteria. Here, we tested all of the predicted KMTs in the cyanobacterium Synechocystis sp. PCC 6803 (Synechocystis), and we biochemically characterized sll1526 that we termed cKMT1 (cyanobacterial lysine methyltransferase 1), and determined that it can catalyze lysine methylation both in vivo and in vitro. Loss of cKMT1 alters photosynthetic electron transfer in Synechocystis. We analyzed cKMT1-regulated methylation sites in Synechocystis using a timsTOF Pro instrument. We identified 305 class I lysine methylation sites within 232 proteins, and of these, 80 methylation sites in 58 proteins were hypomethylated in ΔcKMT1 cells. We further demonstrated that cKMT1 could methylate ferredoxin-NADP(+) oxidoreductase (FNR) and its potential sites of action on FNR were identified. Amino acid residues H118 and Y219 were identified as key residues in the putative active site of cKMT1 as indicated by structure simulation, site-directed mutagenesis, and KMT activity measurement. Using mutations that mimic the unmethylated forms of FNR, we demonstrated that the inability to methylate K139 residues results in a decrease in the redox activity of FNR and affects energy transfer in Synechocystis. Together, our study identified a new KMT in Synechocystis and elucidated a methylation-mediated molecular mechanism catalyzed by cKMT1 for the regulation of energy transfer in cyanobacteria.
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Phukan H, Sarma A, Rex DA, Rai AB, Prasad TS, Madanan MG. Unique Posttranslational Modification Sites of Acetylation, Citrullination, Glutarylation, and Phosphorylation Are Found to Be Specific to the Proteins Partitioned in the Triton X-114 Fractions of Leptospira. ACS OMEGA 2022; 7:18569-18576. [PMID: 35694507 PMCID: PMC9178745 DOI: 10.1021/acsomega.2c01245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/13/2022] [Indexed: 06/15/2023]
Abstract
Posttranslational modifications (PTMs) are decisive factors in the structure, function, and localization of proteins in prokaryotic and eukaryotic organisms. However, prokaryotic organisms lack subcellular organelles, and protein localization based on subcellular locations like cytoplasm, inner membrane, periplasm, and outer membrane can be accounted for functional characterization. We have identified 131 acetylated, 1182 citrullinated, 72 glutarylated, 5 palmitoylated, and 139 phosphorylated proteins from Triton X-114 fractionated proteins of Leptospira, the pathogen of re-emerging zoonotic disease leptospirosis. In total, 74.7% of proteins were found exclusively in different Triton X-114 fractions. Additionally, 21.9% of proteins in multiple fractions had one or more PTM specific to different Triton X-114 fractions. Altogether, 96.6% of proteins showed exclusiveness to different Triton X-114 fractions either due to the presence of the entire protein or with a specific PTM type or position. Further, the PTM distribution within Triton X-114 fractions showed higher acetylation in aqueous, glutarylation in detergent, phosphorylation in pellet, and citrullination in wash fractions representing cytoplasmic, outer membrane, inner membrane, and extracellular locations, respectively. Identification of PTMs in proteins with respect to the subcellular localization will help to characterize candidate proteins before developing novel drugs and vaccines rationally to combat leptospirosis.
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Affiliation(s)
- Homen Phukan
- ICMR-Regional
Medical Research Centre, Port Blair 744103, Andaman and Nicobar
Islands, India
| | - Abhijit Sarma
- ICMR-Regional
Medical Research Centre, Port Blair 744103, Andaman and Nicobar
Islands, India
| | - Devasahayam Arokia
Balaya Rex
- Center
for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangaluru 575018, Karnataka, India
| | - Akhila Balakrishna Rai
- Center
for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangaluru 575018, Karnataka, India
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Rex DAB, Chanderasekaran J, Rai AB, Phukan H, Sarma A, Prasad TSK, Madanan MG. Leptospira and Leptospirosis: New Systems Science Insights on Proteome, Posttranslational Modifications, and Pathogen-Host Interaction. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2022; 26:280-289. [PMID: 35446144 DOI: 10.1089/omi.2022.0007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Leptospirosis is one of the most important zoonotic diseases for planetary health. It is caused by Leptospira spp., which poses a formidable challenge in both rural and urban geographies. Discovery of molecular targets is crucial for developing interventions, including vaccines, against leptospirosis. We report here novel systems science insights on Leptospira proteome, posttranslational modifications (PTMs), and pathogen-host interactions, with an eye to bacterial pathophysiology from a functional standpoint. A systematic reanalysis of unassigned spectra from our previous total proteome identification was used for a multi-PTM search. Notably, we identified 3693 unique high-confidence PTM sites corresponding to 1266 proteins (PTM-profiling probability cutoff value ≥75%). The majority of the phosphorylated peptides were found to be GroEL molecular chaperones. Notably, the molecular docking of PTM-GroEL with STAT3, an important signaling protein in cytokine production, resulted in the prediction of druggable "hotspots." These energetically significant smaller subsets of amino acids (hotspot residues) offer promise for practical applications in planetary health, rational drug design, and peptide engineering. Furthermore, the prediction strategies described here could serve as a starting point for narrowing down the more extensive interface in protein-protein interactions that currently exist. Going forward, systems science approaches and the new insights reported here offer veritable prospects for innovation in preventing and treating leptospirosis.
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Affiliation(s)
- Devasahayam Arokia Balaya Rex
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Jaikanth Chanderasekaran
- Department of Pharmacology, School of Pharmacy and Technology Management, SVKM'S NMIMS University, Hyderabad, India
| | - Akhila Balakrishna Rai
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Homen Phukan
- Department of Biochemistry, ICMR-Regional Medical Research Centre, Port Blair, India
| | - Abhijit Sarma
- Department of Biochemistry, ICMR-Regional Medical Research Centre, Port Blair, India
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Abstract
The two-component system PhoP/PhoQ is essential for Salmonella enterica serovar Typhimurium virulence. Here, we report that PhoP is methylated extensively. Two consecutive glutamate (E) and aspartate (D)/E residues, i.e., E8/D9 and E107/E108, and arginine (R) 112 can be methylated. Individual mutation of these above-mentioned residues caused impaired phosphorylation and dimerization or DNA-binding ability of PhoP to a different extent and led to attenuated bacterial virulence. With the help of specific antibodies recognizing methylated E8 and monomethylated R112, we found that the methylation levels of E8 or R112 decreased dramatically when bacteria encountered low magnesium, acidic pH, or phagocytosis by macrophages, under which PhoP can be activated. Furthermore, CheR, a bacterial chemotaxis methyltransferase, was identified to methylate R112. Overexpression of cheR decreased PhoP activity but increased PhoP stability. Together, the current study reveals that methylation plays an important role in regulating PhoP activities in response to environmental cues and, consequently, modulates Salmonella virulence.
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Abstract
Nε-lysine acetylation is an important, dynamic regulatory posttranslational modification (PTM) that is common in bacteria. Protein acetylomes have been characterized for more than 30 different species, and it is known that acetylation plays important regulatory roles in many essential biological processes. The levels of acetylation are enzymatically controlled by the opposing actions of lysine acetyltransferases and deacetylases. In bacteria, a second mechanism of acetylation exists and occurs via an enzyme-independent manner using the secondary metabolite acetyl-phosphate. Nonenzymatic acetylation accounts for global low levels of acetylation. Recently, studies concerning the role of protein acetylation in bacterial virulence have begun. Acetylated virulence factors have been identified and further characterized. The roles of the enzymes that acetylate and deacetylate proteins in the establishment of infection and biofilm formation have also been investigated. In this review, we discuss the acetylomes of human bacterial pathogens. We highlight examples of known acetylated virulence proteins and examine how they affect survival in the host. Finally, we discuss how acetylation might influence host-pathogen interactions and look at the contribution of acetylation to antimicrobial resistance.
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Applied Proteomics in 'One Health'. Proteomes 2021; 9:proteomes9030031. [PMID: 34208880 PMCID: PMC8293331 DOI: 10.3390/proteomes9030031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 12/19/2022] Open
Abstract
‘One Health’ summarises the idea that human health and animal health are interdependent and bound to the health of ecosystems. The purpose of proteomics methodologies and studies is to determine proteins present in samples of interest and to quantify changes in protein expression during pathological conditions. The objectives of this paper are to review the application of proteomics technologies within the One Health concept and to appraise their role in the elucidation of diseases and situations relevant to One Health. The paper develops in three sections. Proteomics Applications in Zoonotic Infections part discusses proteomics applications in zoonotic infections and explores the use of proteomics for studying pathogenetic pathways, transmission dynamics, diagnostic biomarkers and novel vaccines in prion, viral, bacterial, protozoan and metazoan zoonotic infections. Proteomics Applications in Antibiotic Resistance part discusses proteomics applications in mechanisms of resistance development and discovery of novel treatments for antibiotic resistance. Proteomics Applications in Food Safety part discusses the detection of allergens, exposure of adulteration, identification of pathogens and toxins, study of product traits and characterisation of proteins in food safety. Sensitive analysis of proteins, including low-abundant ones in complex biological samples, will be achieved in the future, thus enabling implementation of targeted proteomics in clinical settings, shedding light on biomarker research and promoting the One Health concept.
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Disentangling the Impact of Sulfur Limitation on Exopolysaccharide and Functionality of Alr2882 by In Silico Approaches in Anabaena sp. PCC 7120. Appl Biochem Biotechnol 2021; 193:1447-1468. [PMID: 33484449 DOI: 10.1007/s12010-021-03501-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 01/07/2021] [Indexed: 01/03/2023]
Abstract
The wide applications, uniqueness, and high quality of cyanobacterial exopolysaccharides (EPSs) have attracted many biotechnologists. Despite it, the inducers and molecular determinants of EPS biosynthesis in cyanobacteria are lesser known. Although, studies revealed that environmental cues especially C/N ratio as the prime modulator, the factors like light, temperature, moisture, and nutrient availability, etc. have been overlooked. Due to this, the possibilities to modify cyanobacterial system for achieving higher quantity of EPS either by modifying growth medium or metabolic engineering are restricted to few optimisations. Therefore, the present work describes the impact of sulfate limitations on the EPS production and compositions in the cyanobacterium Anabaena sp. PCC 7120. Increased EPS production with enhanced expression of alr2882 was observed in lower sulfate supplementations; however, FTIR analysis depicted an altered composition of supramolecule. Furthermore, in silico analysis of Alr2882 depicted the presence of ExoD domain and three transmembrane regions, thereby indicating its membrane localisation and role in the EPS production. Additionally, the phylogeny and multiple sequence alignment showed vertical inheritance of exoD and conservation among cyanobacteria. The meta-threading template-based modelling and ab initio full atomic relaxation by LOMET and ModRefiner servers, respectively, also exhibited helical topology of Alr2882, with nine α-helices arranged antiparallel to the preceding one. Moreover, post-translational modifications predicted in Alr2882 indicated high order of molecular regulation underlining EPS production in Anabaena sp. PCC 7120. This study provides a foundation for understanding the EPS biosynthesis mechanism under sulfur limitation and the possible role of ExoD in cyanobacteria.
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Methylation of two-component response regulator MtrA in mycobacteria negatively modulates its DNA binding and transcriptional activation. Biochem J 2020; 477:4473-4489. [PMID: 33175092 DOI: 10.1042/bcj20200455] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 11/05/2020] [Accepted: 11/11/2020] [Indexed: 12/23/2022]
Abstract
Post-translational modifications such as phosphorylation, nitrosylation, and pupylation modulate multiple cellular processes in Mycobacterium tuberculosis. While protein methylation at lysine and arginine residues is widespread in eukaryotes, to date only two methylated proteins in Mtb have been identified. Here, we report the identification of methylation at lysine and/or arginine residues in nine mycobacterial proteins. Among the proteins identified, we chose MtrA, an essential response regulator of a two-component signaling system, which gets methylated on multiple lysine and arginine residues to examine the functional consequences of methylation. While methylation of K207 confers a marginal decrease in the DNA-binding ability of MtrA, methylation of R122 or K204 significantly reduces the interaction with the DNA. Overexpression of S-adenosyl homocysteine hydrolase (SahH), an enzyme that modulates the levels of S-adenosyl methionine in mycobacteria decreases the extent of MtrA methylation. Most importantly, we show that decreased MtrA methylation results in transcriptional activation of mtrA and sahH promoters. Collectively, we identify novel methylated proteins, expand the list of modifications in mycobacteria by adding arginine methylation, and show that methylation regulates MtrA activity. We propose that protein methylation could be a more prevalent modification in mycobacterial proteins.
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10
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Forrest S, Welch M. Arming the troops: Post-translational modification of extracellular bacterial proteins. Sci Prog 2020; 103:36850420964317. [PMID: 33148128 PMCID: PMC10450907 DOI: 10.1177/0036850420964317] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Protein secretion is almost universally employed by bacteria. Some proteins are retained on the cell surface, whereas others are released into the extracellular milieu, often playing a key role in virulence. In this review, we discuss the diverse types and potential functions of post-translational modifications (PTMs) occurring to extracellular bacterial proteins.
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Affiliation(s)
- Suzanne Forrest
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Martin Welch
- Department of Biochemistry, University of Cambridge, Cambridge, UK
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11
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Thoduvayil S, Dhandapani G, Brahma R, Devasahayam Arokia Balaya R, Mangalaparthi KK, Patel K, Kumar M, Tennyson J, Satheeshkumar PK, Kulkarni MJ, Pinto SM, Prasad TSK, Madanan MG. Triton X-114 Fractionated Subcellular Proteome of Leptospira interrogans Shows Selective Enrichment of Pathogenic and Outer Membrane Proteins in the Detergent Fraction. Proteomics 2020; 20:e2000170. [PMID: 32846045 DOI: 10.1002/pmic.202000170] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/30/2020] [Indexed: 12/28/2022]
Abstract
The Triton X-114-based solubilization and temperature-dependent phase separation of proteins is used for subcellular fractionation where, aqueous, detergent, and pellet fractions represents cytoplasmic, outer membrane (OM), and inner membrane proteins, respectively. Mass spectrometry-based proteomic analysis of Triton X-114 fractions of proteomic analysis of Leptospira interrogans identified 2957 unique proteins distributed across the fractions. The results are compared with bioinformatics predictions on their subcellular localization and pathogenic nature. Analysis of the distribution of proteins across the Triton X-114 fractions with the predicted characteristics is performed based on "number" of unique type of proteins, and "quantity" which represents the amount of unique protein. The highest number of predicted outer membrane proteins (OMPs) and pathogenic proteins are found in aqueous and pellet fractions, whereas detergent fraction representing the OM has the highest quantity of OMPs and pathogenic proteins though lower in number than the aqueous and pellet fractions. This leaves the possibility of an upsurge in pathogenic proteins and OMPs on the OM under pathogenic conditions suggesting their potential use to combat leptospirosis. Further, the Triton X-114 subcellular fractions are more correlated to enrichment of pathogenic proteins predicted by MP3 software than predicted localization.
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Affiliation(s)
- Sikha Thoduvayil
- Indian Council of Medical Research, Regional Medical Research Centre Port Blair, Dollygunj, Port Blair, 744103, India.,Department of Pathology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, 605006, India
| | - Gunasekaran Dhandapani
- Indian Council of Medical Research, Regional Medical Research Centre Port Blair, Dollygunj, Port Blair, 744103, India.,Department of Chemical Sciences, Ariel University, Ariel, 70400, Israel
| | - Rahul Brahma
- Indian Council of Medical Research, Regional Medical Research Centre Port Blair, Dollygunj, Port Blair, 744103, India
| | - Rex Devasahayam Arokia Balaya
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangaluru, 575018, India
| | - Kiran K Mangalaparthi
- Institute of Bioinformatics, International Technology Park, Bengaluru, 560066, India.,NIMHANS-IOB Proteomics and Bioinformatics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences, Bengaluru, 560029, India
| | - Krishna Patel
- Institute of Bioinformatics, International Technology Park, Bengaluru, 560066, India.,Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, 690525, India
| | - Manish Kumar
- Institute of Bioinformatics, International Technology Park, Bengaluru, 560066, India.,Manipal Academy of Higher Education, Manipal, 576104, India
| | - Jebasingh Tennyson
- School of Biological Sciences, Madurai Kamaraj University, Madurai, 625021, India
| | - P K Satheeshkumar
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Mahesh J Kulkarni
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, 411008, India
| | - Sneha M Pinto
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangaluru, 575018, India.,Institute of Bioinformatics, International Technology Park, Bengaluru, 560066, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangaluru, 575018, India.,Institute of Bioinformatics, International Technology Park, Bengaluru, 560066, India.,NIMHANS-IOB Proteomics and Bioinformatics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences, Bengaluru, 560029, India
| | - Madathiparambil G Madanan
- Indian Council of Medical Research, Regional Medical Research Centre Port Blair, Dollygunj, Port Blair, 744103, India
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12
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Vozáriková V, Kunová N, Bauer JA, Frankovský J, Kotrasová V, Procházková K, Džugasová V, Kutejová E, Pevala V, Nosek J, Tomáška Ľ. Mitochondrial HMG-Box Containing Proteins: From Biochemical Properties to the Roles in Human Diseases. Biomolecules 2020; 10:biom10081193. [PMID: 32824374 PMCID: PMC7463775 DOI: 10.3390/biom10081193] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 08/11/2020] [Accepted: 08/13/2020] [Indexed: 12/14/2022] Open
Abstract
Mitochondrial DNA (mtDNA) molecules are packaged into compact nucleo-protein structures called mitochondrial nucleoids (mt-nucleoids). Their compaction is mediated in part by high-mobility group (HMG)-box containing proteins (mtHMG proteins), whose additional roles include the protection of mtDNA against damage, the regulation of gene expression and the segregation of mtDNA into daughter organelles. The molecular mechanisms underlying these functions have been identified through extensive biochemical, genetic, and structural studies, particularly on yeast (Abf2) and mammalian mitochondrial transcription factor A (TFAM) mtHMG proteins. The aim of this paper is to provide a comprehensive overview of the biochemical properties of mtHMG proteins, the structural basis of their interaction with DNA, their roles in various mtDNA transactions, and the evolutionary trajectories leading to their rapid diversification. We also describe how defects in the maintenance of mtDNA in cells with dysfunctional mtHMG proteins lead to different pathologies at the cellular and organismal level.
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Affiliation(s)
- Veronika Vozáriková
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina B-1, 842 15 Bratislava, Slovakia; (V.V.); (J.F.); (K.P.); (V.D.)
| | - Nina Kunová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia; (N.K.); (J.A.B.); (V.K.); (E.K.); (V.P.)
| | - Jacob A. Bauer
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia; (N.K.); (J.A.B.); (V.K.); (E.K.); (V.P.)
| | - Ján Frankovský
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina B-1, 842 15 Bratislava, Slovakia; (V.V.); (J.F.); (K.P.); (V.D.)
| | - Veronika Kotrasová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia; (N.K.); (J.A.B.); (V.K.); (E.K.); (V.P.)
| | - Katarína Procházková
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina B-1, 842 15 Bratislava, Slovakia; (V.V.); (J.F.); (K.P.); (V.D.)
| | - Vladimíra Džugasová
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina B-1, 842 15 Bratislava, Slovakia; (V.V.); (J.F.); (K.P.); (V.D.)
| | - Eva Kutejová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia; (N.K.); (J.A.B.); (V.K.); (E.K.); (V.P.)
| | - Vladimír Pevala
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia; (N.K.); (J.A.B.); (V.K.); (E.K.); (V.P.)
| | - Jozef Nosek
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina CH-1, 842 15 Bratislava, Slovakia;
| | - Ľubomír Tomáška
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina B-1, 842 15 Bratislava, Slovakia; (V.V.); (J.F.); (K.P.); (V.D.)
- Correspondence: ; Tel.: +421-2-90149-433
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13
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Putz EJ, Nally JE. Investigating the Immunological and Biological Equilibrium of Reservoir Hosts and Pathogenic Leptospira: Balancing the Solution to an Acute Problem? Front Microbiol 2020; 11:2005. [PMID: 32922382 PMCID: PMC7456838 DOI: 10.3389/fmicb.2020.02005] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 07/29/2020] [Indexed: 12/18/2022] Open
Abstract
Leptospirosis is a devastating zoonotic disease affecting people and animals across the globe. Pathogenic leptospires are excreted in urine of reservoir hosts which directly or indirectly leads to continued disease transmission, via contact with mucous membranes or a breach of the skin barrier of another host. Human fatalities approach 60,000 deaths per annum; though most vertebrates are susceptible to leptospirosis, complex interactions between host species and serovars of Leptospira can yield disease phenotypes that vary from asymptomatic shedding in reservoir hosts, to multi-organ failure in incidental hosts. Clinical symptoms of acute leptospirosis reflect the diverse range of pathogenic species and serovars that cause infection, the level of exposure, and the relationship of the pathogen with the given host. However, in all cases, pathogenic Leptospira are excreted into the environment via urine from reservoir hosts which are uniformly recognized as asymptomatic carriers. Therefore, the reservoir host serves as the cornerstone of persistent disease transmission. Although bacterin vaccines can be used to abate renal carriage and excretion in domestic animal species, there is an urgent need to advance our understanding of immune-mediated host–pathogen interactions that facilitate persistent asymptomatic carriage. This review summarizes the current understanding of host–pathogen interactions in the reservoir host and prioritizes research to unravel mechanisms that allow for colonization but not destruction of the host. This information is required to understand, and ultimately control, the transmission of pathogenic Leptospira.
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Affiliation(s)
- Ellie J Putz
- Infectious Bacterial Diseases Research Unit, National Animal Disease Center, United States Department of Agriculture, Agricultural Research Service, Ames, IA, United States
| | - Jarlath E Nally
- Infectious Bacterial Diseases Research Unit, National Animal Disease Center, United States Department of Agriculture, Agricultural Research Service, Ames, IA, United States
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14
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Bonne Køhler J, Jers C, Senissar M, Shi L, Derouiche A, Mijakovic I. Importance of protein Ser/Thr/Tyr phosphorylation for bacterial pathogenesis. FEBS Lett 2020; 594:2339-2369. [PMID: 32337704 DOI: 10.1002/1873-3468.13797] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 04/16/2020] [Accepted: 04/20/2020] [Indexed: 12/13/2022]
Abstract
Protein phosphorylation regulates a large variety of biological processes in all living cells. In pathogenic bacteria, the study of serine, threonine, and tyrosine (Ser/Thr/Tyr) phosphorylation has shed light on the course of infectious diseases, from adherence to host cells to pathogen virulence, replication, and persistence. Mass spectrometry (MS)-based phosphoproteomics has provided global maps of Ser/Thr/Tyr phosphosites in bacterial pathogens. Despite recent developments, a quantitative and dynamic view of phosphorylation events that occur during bacterial pathogenesis is currently lacking. Temporal, spatial, and subpopulation resolution of phosphorylation data is required to identify key regulatory nodes underlying bacterial pathogenesis. Herein, we discuss how technological improvements in sample handling, MS instrumentation, data processing, and machine learning should improve bacterial phosphoproteomic datasets and the information extracted from them. Such information is expected to significantly extend the current knowledge of Ser/Thr/Tyr phosphorylation in pathogenic bacteria and should ultimately contribute to the design of novel strategies to combat bacterial infections.
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Affiliation(s)
- Julie Bonne Køhler
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Carsten Jers
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Mériem Senissar
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Lei Shi
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Abderahmane Derouiche
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Ivan Mijakovic
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.,Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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15
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Cambridge SB. Hypothesis: protein and RNA attributes are continuously optimized over time. BMC Genomics 2019; 20:1012. [PMID: 31870287 PMCID: PMC6929361 DOI: 10.1186/s12864-019-6371-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 12/05/2019] [Indexed: 02/01/2023] Open
Abstract
Background Little is known why proteins and RNAs exhibit half-lives varying over several magnitudes. Despite many efforts, a conclusive link between half-lives and gene function could not be established suggesting that other determinants may influence these molecular attributes. Results Here, I find that with increasing gene age there is a gradual and significant increase of protein and RNA half-lives, protein structure, and other molecular attributes that tend to affect protein abundance. These observations are accommodated in a hypothesis which posits that new genes at ‘birth’ are not optimized and thus their products exhibit low half-lives and less structure but continuous mutagenesis eventually improves these attributes. Thus, the protein and RNA products of the oldest genes obtained their high degrees of stability and structure only after billions of years while the products of younger genes had less time to be optimized and are therefore less stable and structured. Because more stable proteins with lower turnover require less transcription to maintain the same level of abundance, reduced transcription-associated mutagenesis (TAM) would fixate the changes by increasing gene conservation. Conclusions Consequently, the currently observed diversity of molecular attributes is a snapshot of gene products being at different stages along their temporal path of optimization.
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Affiliation(s)
- Sidney B Cambridge
- Department of Functional Neuroanatomy, Heidelberg University, Heidelberg, Germany.
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16
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Abstract
This chapter covers the progress made in the Leptospira field since the application of mutagenesis techniques and how they have allowed the study of virulence factors and, more generally, the biology of Leptospira. The last decade has seen advances in our ability to perform molecular genetic analysis of Leptospira. Major achievements include the generation of large collections of mutant strains and the construction of replicative plasmids, enabling complementation of mutations. However, there are still no practical tools for routine genetic manipulation of pathogenic Leptospira strains, slowing down advances in pathogenesis research. This review summarizes the status of the molecular genetic toolbox for Leptospira species and highlights new challenges in the nascent field of Leptospira genetics.
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Affiliation(s)
- Mathieu Picardeau
- Biology of Spirochetes Unit, Institut Pasteur, 28 Rue Du Docteur Roux, 75724, Paris Cedex 15, France.
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17
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Post-translational modification of nucleoid-associated proteins: an extra layer of functional modulation in bacteria? Biochem Soc Trans 2018; 46:1381-1392. [PMID: 30287510 DOI: 10.1042/bst20180488] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 08/31/2018] [Accepted: 09/04/2018] [Indexed: 01/08/2023]
Abstract
Post-translational modification (PTM) of histones has been investigated in eukaryotes for years, revealing its widespread occurrence and functional importance. Many PTMs affect chromatin folding and gene activity. Only recently the occurrence of such modifications has been recognized in bacteria. However, it is unclear whether PTM of the bacterial counterparts of eukaryotic histones, nucleoid-associated proteins (NAPs), bears a comparable significance. Here, we scrutinize proteome mass spectrometry data for PTMs of the four most abundantly present NAPs in Escherichia coli (H-NS, HU, IHF and FIS). This approach allowed us to identify a total of 101 unique PTMs in the 11 independent proteomic studies covered in this review. Combined with structural and genetic information on these proteins, we describe potential effects of these modifications (perturbed DNA-binding, structural integrity or interaction with other proteins) on their function.
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18
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Nascimento Filho EG, Vieira ML, Teixeira AF, Santos JC, Fernandes LGV, Passalia FJ, Daroz BB, Rossini A, Kochi LT, Cavenague MF, Pimenta DC, Nascimento ALTO. Proteomics as a tool to understand Leptospira physiology and virulence: Recent advances, challenges and clinical implications. J Proteomics 2018; 180:80-87. [PMID: 29501847 DOI: 10.1016/j.jprot.2018.02.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 02/14/2018] [Accepted: 02/22/2018] [Indexed: 01/24/2023]
Affiliation(s)
- Edson G Nascimento Filho
- Laboratório Especial de Desenvolvimento de Vacinas, Instituto Butantan, Avenida Vital Brazil, 1500, 05503-900 Sao Paulo, SP, Brazil
| | - Monica L Vieira
- Laboratório Especial de Desenvolvimento de Vacinas, Instituto Butantan, Avenida Vital Brazil, 1500, 05503-900 Sao Paulo, SP, Brazil
| | - Aline F Teixeira
- Laboratório Especial de Desenvolvimento de Vacinas, Instituto Butantan, Avenida Vital Brazil, 1500, 05503-900 Sao Paulo, SP, Brazil
| | - Jademilson C Santos
- Laboratório Especial de Desenvolvimento de Vacinas, Instituto Butantan, Avenida Vital Brazil, 1500, 05503-900 Sao Paulo, SP, Brazil
| | - Luis G V Fernandes
- Laboratório Especial de Desenvolvimento de Vacinas, Instituto Butantan, Avenida Vital Brazil, 1500, 05503-900 Sao Paulo, SP, Brazil
| | - Felipe J Passalia
- Laboratório Especial de Desenvolvimento de Vacinas, Instituto Butantan, Avenida Vital Brazil, 1500, 05503-900 Sao Paulo, SP, Brazil; Programa de Pos-Graduação Interunidades em Biotecnologia, Instituto de Ciências Biomédicas, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Brenda B Daroz
- Laboratório Especial de Desenvolvimento de Vacinas, Instituto Butantan, Avenida Vital Brazil, 1500, 05503-900 Sao Paulo, SP, Brazil; Programa de Pos-Graduação Interunidades em Biotecnologia, Instituto de Ciências Biomédicas, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Amanda Rossini
- Laboratório Especial de Desenvolvimento de Vacinas, Instituto Butantan, Avenida Vital Brazil, 1500, 05503-900 Sao Paulo, SP, Brazil; Programa de Pos-Graduação Interunidades em Biotecnologia, Instituto de Ciências Biomédicas, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Leandro T Kochi
- Laboratório Especial de Desenvolvimento de Vacinas, Instituto Butantan, Avenida Vital Brazil, 1500, 05503-900 Sao Paulo, SP, Brazil; Programa de Pos-Graduação Interunidades em Biotecnologia, Instituto de Ciências Biomédicas, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Maria F Cavenague
- Laboratório Especial de Desenvolvimento de Vacinas, Instituto Butantan, Avenida Vital Brazil, 1500, 05503-900 Sao Paulo, SP, Brazil; Programa de Pos-Graduação Interunidades em Biotecnologia, Instituto de Ciências Biomédicas, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Daniel C Pimenta
- Laboratório de Bioquímica e Biofísica, Instituto Butantan, Avenida Vital Brazil, 1500, 05503-900 Sao Paulo, SP, Brazil
| | - Ana L T O Nascimento
- Laboratório Especial de Desenvolvimento de Vacinas, Instituto Butantan, Avenida Vital Brazil, 1500, 05503-900 Sao Paulo, SP, Brazil.
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19
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Outer Membrane Protein OmpB Methylation May Mediate Bacterial Virulence. Trends Biochem Sci 2017; 42:936-945. [PMID: 29037863 DOI: 10.1016/j.tibs.2017.09.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 09/16/2017] [Accepted: 09/20/2017] [Indexed: 12/29/2022]
Abstract
Methylation of outer membrane proteins (OMPs) has been implicated in bacterial virulence. Lysine methylation in rickettsial OmpB is correlated with rickettsial virulence, and N- and O-methylations are also observed in virulence-relevant OMPs from several pathogenic bacteria that cause typhus, leptospirosis, tuberculosis, and anaplasmosis. We summarize recent findings on the structure of methylated OmpB, biochemical characterization, and crystal structures of OmpB methyltransferases. Native rickettsial OmpB purified from highly virulent strains contains multiple clusters of trimethyllysine, in contrast with mostly monomethyllysine, and no trimethyllysine is found in an avirulent strain. Crystal structure of the methyltransferases reveals mechanistic insights for catalysis, and a working model is discussed for this unusual post-translational modification.
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20
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Nally JE, Grassmann AA, Planchon S, Sergeant K, Renaut J, Seshu J, McBride AJ, Caimano MJ. Pathogenic Leptospires Modulate Protein Expression and Post-translational Modifications in Response to Mammalian Host Signals. Front Cell Infect Microbiol 2017; 7:362. [PMID: 28848720 PMCID: PMC5553009 DOI: 10.3389/fcimb.2017.00362] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 07/26/2017] [Indexed: 12/24/2022] Open
Abstract
Pathogenic species of Leptospira cause leptospirosis, a bacterial zoonotic disease with a global distribution affecting over one million people annually. Reservoir hosts of leptospirosis, including rodents, dogs, and cattle, exhibit little to no signs of disease but shed large numbers of organisms in their urine. Transmission occurs when mucosal surfaces or abraded skin come into contact with infected urine or urine-contaminated water or soil. Whilst little is known about how Leptospira adapt to and persist within a reservoir host, in vitro studies suggest that leptospires alter their transcriptomic and proteomic profiles in response to environmental signals encountered during mammalian infection. We applied the dialysis membrane chamber (DMC) peritoneal implant model to compare the whole cell proteome of in vivo derived leptospires with that of leptospires cultivated in vitro at 30°C and 37°C by 2-dimensional difference in-gel electrophoresis (2-D DIGE). Of 1,735 protein spots aligned across 9 2-D DIGE gels, 202 protein spots were differentially expressed (p < 0.05, fold change >1.25 or < −1.25) across all three conditions. Differentially expressed proteins were excised for identification by mass spectrometry. Data are available via ProteomeXchange with identifier PXD006995. The greatest differences were detected when DMC-cultivated leptospires were compared with IV30- or IV37-cultivated leptospires, including the increased expression of multiple isoforms of Loa22, a known virulence factor. Unexpectedly, 20 protein isoforms of LipL32 and 7 isoforms of LipL41 were uniformly identified by DIGE as differentially expressed, suggesting that unique post-translational modifications (PTMs) are operative in response to mammalian host conditions. To test this hypothesis, a rat model of persistent renal colonization was used to isolate leptospires directly from the urine of experimentally infected rats. Comparison of urinary derived leptospires to IV30 leptospires by 2-D immunoblotting confirmed that modification of proteins with trimethyllysine and acetyllysine occurs to a different degree in response to mammalian host signals encountered during persistent renal colonization. These results provide novel insights into differential protein and PTMs present in response to mammalian host signals which can be used to further define the unique equilibrium that exists between pathogenic leptospires and their reservoir host of infection.
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Affiliation(s)
- Jarlath E Nally
- Infectious Bacterial Diseases Research, National Animal Disease Center, United States Department of Agriculture, Agricultural Research ServiceAmes, IA, United States
| | - Andre A Grassmann
- Biotechnology Unit, Technological Development Center, Federal University of PelotasPelotas, Brazil.,Departments of Medicine, Pediatrics, and Molecular Biology and Biophysics, University of Connecticut Health CenterFarmington, CT, United States
| | - Sébastien Planchon
- Environmental Research and Innovation Department, Luxembourg Institute of Science and TechnologyBelvaux, Luxembourg
| | - Kjell Sergeant
- Environmental Research and Innovation Department, Luxembourg Institute of Science and TechnologyBelvaux, Luxembourg
| | - Jenny Renaut
- Environmental Research and Innovation Department, Luxembourg Institute of Science and TechnologyBelvaux, Luxembourg
| | - Janakiram Seshu
- Department of Biology, University of Texas San AntoniaSan Antonia, TX, United States
| | - Alan J McBride
- Biotechnology Unit, Technological Development Center, Federal University of PelotasPelotas, Brazil.,Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Ministry of HealthSalvador, Brazil
| | - Melissa J Caimano
- Departments of Medicine, Pediatrics, and Molecular Biology and Biophysics, University of Connecticut Health CenterFarmington, CT, United States
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22
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Abstract
Lipoproteins are lipid-modified proteins that dominate the spirochetal proteome. While found in all bacteria, spirochetal lipoproteins have unique features and play critical roles in spirochete biology. For this reason, considerable effort has been devoted to determining how the lipoproteome is generated. Essential features of the structural elements of lipoproteins are now understood with greater clarity, enabling greater confidence in identification of lipoproteins from genomic sequences. The journey from the ribosome to the outer membrane, and in some cases, to the cellular surface has been defined, including secretion, lipidation, sorting, and export across the outer membrane. Given their abundance and importance, it is not surprising that spirochetes have developed a number of strategies for regulating the spatiotemporal expression of lipoproteins. In some cases, lipoprotein expression is tied to various environmental cues, while in other cases, it is linked to growth rate. This regulation enables spirochetes to express certain lipoproteins at high levels in one phase of the spirochete lifecycle, while dramatically downregulating the same lipoproteins in other phases. The mammalian host has developed specialized mechanisms for recognizing lipoproteins and triggering an immune response. Evasion of that immune response is essential for spirochete persistence. For this reason, spirochetes have developed mechanisms for altering lipoproteins. Lipoproteins recognized by antibodies formed during infection are key serodiagnostic antigens. In addition, lipoprotein vaccines have been developed for generating an immune response to control or prevent a spirochete infection. This chapter summarizes our current understanding of lipoproteins in interactions of spirochetes with their hosts.
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23
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Bastos PAD, da Costa JP, Vitorino R. A glimpse into the modulation of post-translational modifications of human-colonizing bacteria. J Proteomics 2016; 152:254-275. [PMID: 27888141 DOI: 10.1016/j.jprot.2016.11.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 10/22/2016] [Accepted: 11/07/2016] [Indexed: 12/19/2022]
Abstract
Protein post-translational modifications (PTMs) are a key bacterial feature that holds the capability to modulate protein function and responses to environmental cues. Until recently, their role in the regulation of prokaryotic systems has been largely neglected. However, the latest developments in mass spectrometry-based proteomics have allowed an unparalleled identification and quantification of proteins and peptides that undergo PTMs in bacteria, including in species which directly or indirectly affect human health. Herein, we address this issue by carrying out the largest and most comprehensive global pooling and comparison of PTM peptides and proteins from bacterial species performed to date. Data was collected from 91 studies relating to PTM bacterial peptides or proteins identified by mass spectrometry-based methods. The present analysis revealed that there was a considerable overlap between PTMs across species, especially between acetylation and other PTMs, particularly succinylation. Phylogenetically closer species may present more overlapping phosphoproteomes, but environmental triggers also contribute to this proximity. PTMs among bacteria were found to be extremely versatile and diverse, meaning that the same protein may undergo a wide variety of different modifications across several species, but it could also suffer different modifications within the same species.
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Affiliation(s)
- Paulo André Dias Bastos
- Department of Medical Sciences, Institute for Biomedicine-iBiMED, University of Aveiro, Aveiro, Portugal; Department of Chemistry, University of Aveiro, Portugal
| | | | - Rui Vitorino
- Department of Medical Sciences, Institute for Biomedicine-iBiMED, University of Aveiro, Aveiro, Portugal; Department of Physiology and Cardiothoracic Surgery, Faculty of Medicine, University of Porto, Porto, Portugal.
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24
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Zhang J, Yang MK, Zeng H, Ge F. GAPP: A Proteogenomic Software for Genome Annotation and Global Profiling of Post-translational Modifications in Prokaryotes. Mol Cell Proteomics 2016; 15:3529-3539. [PMID: 27630248 DOI: 10.1074/mcp.m116.060046] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Indexed: 11/06/2022] Open
Abstract
Although the number of sequenced prokaryotic genomes is growing rapidly, experimentally verified annotation of prokaryotic genome remains patchy and challenging. To facilitate genome annotation efforts for prokaryotes, we developed an open source software called GAPP for genome annotation and global profiling of post-translational modifications (PTMs) in prokaryotes. With a single command, it provides a standard workflow to validate and refine predicted genetic models and discover diverse PTM events. We demonstrated the utility of GAPP using proteomic data from Helicobacter pylori, one of the major human pathogens that is responsible for many gastric diseases. Our results confirmed 84.9% of the existing predicted H. pylori proteins, identified 20 novel protein coding genes, and corrected four existing gene models with regard to translation initiation sites. In particular, GAPP revealed a large repertoire of PTMs using the same proteomic data and provided a rich resource that can be used to examine the functions of reversible modifications in this human pathogen. This software is a powerful tool for genome annotation and global discovery of PTMs and is applicable to any sequenced prokaryotic organism; we expect that it will become an integral part of ongoing genome annotation efforts for prokaryotes. GAPP is freely available at https://sourceforge.net/projects/gappproteogenomic/.
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Affiliation(s)
- Jia Zhang
- From the ‡Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Ming-Kun Yang
- From the ‡Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Honghui Zeng
- §Wuhan Branch, Supercomputing Center, Chinese Academy of Sciences, China
| | - Feng Ge
- From the ‡Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; .,§Wuhan Branch, Supercomputing Center, Chinese Academy of Sciences, China
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25
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Ouidir T, Jouenne T, Hardouin J. Post-translational modifications in Pseudomonas aeruginosa revolutionized by proteomic analysis. Biochimie 2016; 125:66-74. [PMID: 26952777 DOI: 10.1016/j.biochi.2016.03.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 03/01/2016] [Indexed: 11/25/2022]
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that causes severe infections in vulnerable individuals. It is known that post-translational modifications (PTMs) play a key role in bacterial physiology. Their characterization is still challenging and the recent advances in proteomics allow large-scale and high-throughput analyses of PTMs. Here, we provide an overview of proteomic data about the modified proteins in P. aeruginosa. We emphasize the significant contribution of proteomics in knowledge enhancement of PTMs (phosphorylation, N-acetylation and glycosylation) and we discuss their importance in P. aeruginosa physiology.
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Affiliation(s)
- Tassadit Ouidir
- CNRS, UMR 6270, Polymères, Biopolymères, Surfaces Laboratory, F-76820 Mont-Saint-Aignan, France; Normandie Univ, UR, France; PISSARO Proteomic Facility, IRIB, F-76820 Mont-Saint-Aignan, France
| | - Thierry Jouenne
- CNRS, UMR 6270, Polymères, Biopolymères, Surfaces Laboratory, F-76820 Mont-Saint-Aignan, France; Normandie Univ, UR, France; PISSARO Proteomic Facility, IRIB, F-76820 Mont-Saint-Aignan, France
| | - Julie Hardouin
- CNRS, UMR 6270, Polymères, Biopolymères, Surfaces Laboratory, F-76820 Mont-Saint-Aignan, France; Normandie Univ, UR, France; PISSARO Proteomic Facility, IRIB, F-76820 Mont-Saint-Aignan, France.
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26
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Xiong Q, Chen Z, Ge F. Proteomic analysis of post translational modifications in cyanobacteria. J Proteomics 2016; 134:57-64. [DOI: 10.1016/j.jprot.2015.07.037] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 06/28/2015] [Accepted: 07/30/2015] [Indexed: 01/16/2023]
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27
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Ouidir T, Kentache T, Hardouin J. Protein lysine acetylation in bacteria: Current state of the art. Proteomics 2015; 16:301-9. [DOI: 10.1002/pmic.201500258] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 08/11/2015] [Accepted: 09/15/2015] [Indexed: 12/28/2022]
Affiliation(s)
- Tassadit Ouidir
- CNRS, UMR 6270, Polymères, Biopolymères; Surfaces Laboratory; Mont-Saint-Aignan France
- Normandie University; UR France
- PISSARO proteomic facility; IRIB; Mont-Saint-Aignan France
| | - Takfarinas Kentache
- CNRS, UMR 6270, Polymères, Biopolymères; Surfaces Laboratory; Mont-Saint-Aignan France
- Normandie University; UR France
- PISSARO proteomic facility; IRIB; Mont-Saint-Aignan France
| | - Julie Hardouin
- CNRS, UMR 6270, Polymères, Biopolymères; Surfaces Laboratory; Mont-Saint-Aignan France
- Normandie University; UR France
- PISSARO proteomic facility; IRIB; Mont-Saint-Aignan France
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28
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Multiple Posttranslational Modifications of Leptospira biflexa Proteins as Revealed by Proteomic Analysis. Appl Environ Microbiol 2015; 82:1183-1195. [PMID: 26655756 DOI: 10.1128/aem.03056-15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 12/01/2015] [Indexed: 12/12/2022] Open
Abstract
The saprophyte Leptospira biflexa is an excellent model for studying the physiology of the medically important Leptospira genus, the pathogenic members of which are more recalcitrant to genetic manipulation and have significantly slower in vitro growth. However, relatively little is known regarding the proteome of L. biflexa, limiting its utility as a model for some studies. Therefore, we have generated a proteomic map of both soluble and membrane-associated proteins of L. biflexa during exponential growth and in stationary phase. Using these data, we identified abundantly produced proteins in each cellular fraction and quantified the transcript levels from a subset of these genes using quantitative reverse transcription-PCR (RT-PCR). These proteins should prove useful as cellular markers and as controls for gene expression studies. We also observed a significant number of L. biflexa membrane-associated proteins with multiple isoforms, each having unique isoelectric focusing points. L. biflexa cell lysates were examined for several posttranslational modifications suggested by the protein patterns. Methylation and acetylation of lysine residues were predominately observed in the proteins of the membrane-associated fraction, while phosphorylation was detected mainly among soluble proteins. These three posttranslational modification systems appear to be conserved between the free-living species L. biflexa and the pathogenic species Leptospira interrogans, suggesting an important physiological advantage despite the varied life cycles of the different species.
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29
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Oliveira TL, Grassmann AA, Schuch RA, Seixas Neto ACP, Mendonça M, Hartwig DD, McBride AJA, Dellagostin OA. Evaluation of the Leptospira interrogans Outer Membrane Protein OmpL37 as a Vaccine Candidate. PLoS One 2015; 10:e0142821. [PMID: 26588685 PMCID: PMC4654524 DOI: 10.1371/journal.pone.0142821] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 10/27/2015] [Indexed: 12/22/2022] Open
Abstract
The identification of potential vaccine candidates against leptospirosis remains a challenge. However, one such candidate is OmpL37, a potentially surface-exposed antigen that has the highest elastin-binding ability described to date, suggesting that it plays an important role in host colonization. In order to evaluate OmpL37's ability to induce a protective immune response, prime-boost, DNA and subunit vaccine strategies were tested in the hamster model of lethal leptospirosis. The humoral immune response was evaluated using an indirect ELISA test, and the cytokine profile in whole blood was determined by quantitative real-time PCR. Unlike the DNA vaccine, the administration of recombinant OmpL37 induced a strong IgG antibody response. When individually administrated, both formulations stimulated a TNF-α mediated inflammatory response. However, none of the OmpL37 formulations or vaccination strategies induced protective immunity. Further studies are required towards the identification of new vaccine targets against leptospirosis.
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Affiliation(s)
- Thaís Larré Oliveira
- Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - André Alex Grassmann
- Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Rodrigo Andrade Schuch
- Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Amilton Clair Pinto Seixas Neto
- Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Marcelo Mendonça
- Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Daiane Drawanz Hartwig
- Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
- Departamento de Microbiologia e Parasitologia, Instituto de Biologia, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Alan John Alexander McBride
- Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Odir Antônio Dellagostin
- Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
- * E-mail:
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Mo R, Yang M, Chen Z, Cheng Z, Yi X, Li C, He C, Xiong Q, Chen H, Wang Q, Ge F. Acetylome analysis reveals the involvement of lysine acetylation in photosynthesis and carbon metabolism in the model cyanobacterium Synechocystis sp. PCC 6803. J Proteome Res 2015; 14:1275-86. [PMID: 25621733 DOI: 10.1021/pr501275a] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Cyanobacteria are the oldest known life form inhabiting Earth and the only prokaryotes capable of performing oxygenic photosynthesis. Synechocystis sp. PCC 6803 (Synechocystis) is a model cyanobacterium used extensively in research on photosynthesis and environmental adaptation. Posttranslational protein modification by lysine acetylation plays a critical regulatory role in both eukaryotes and prokaryotes; however, its extent and function in cyanobacteria remain unexplored. Herein, we performed a global acetylome analysis on Synechocystis through peptide prefractionation, antibody enrichment, and high accuracy LC-MS/MS analysis; identified 776 acetylation sites on 513 acetylated proteins; and functionally categorized them into an interaction map showing their involvement in various biological processes. Consistent with previous reports, a large fraction of the acetylation sites are present on proteins involved in cellular metabolism. Interestingly, for the first time, many proteins involved in photosynthesis, including the subunits of phycocyanin (CpcA, CpcB, CpcC, and CpcG) and allophycocyanin (ApcA, ApcB, ApcD, ApcE, and ApcF), were found to be lysine acetylated, suggesting that lysine acetylation may play regulatory roles in the photosynthesis process. Six identified acetylated proteins associated with photosynthesis and carbon metabolism were further validated by immunoprecipitation and Western blotting. Our data provide the first global survey of lysine acetylation in cyanobacteria and reveal previously unappreciated roles of lysine acetylation in the regulation of photosynthesis. The provided data set may serve as an important resource for the functional analysis of lysine acetylation in cyanobacteria and facilitate the elucidation of the entire metabolic networks and photosynthesis process in this model cyanobacterium.
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Affiliation(s)
- Ran Mo
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences , Wuhan 430072, China
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Abstract
The outer membrane (OM) is the front line of leptospiral interactions with their environment and the mammalian host. Unlike most invasive spirochetes, pathogenic leptospires must be able to survive in both free-living and host-adapted states. As organisms move from one set of environmental conditions to another, the OM must cope with a series of conflicting challenges. For example, the OM must be porous enough to allow nutrient uptake, yet robust enough to defend the cell against noxious substances. In the host, the OM presents a surface decorated with adhesins and receptors for attaching to, and acquiring, desirable host molecules such as the complement regulator, Factor H.Factor H. On the other hand, the OM must enable leptospires to evade detection by the host's immune system on their way from sites of invasion through the bloodstream to the protected niche of the proximal tubule. The picture that is emerging of the leptospiral OM is that, while it shares many of the characteristics of the OMs of spirochetes and Gram-negative bacteria, it is also unique and different in ways that make it of general interest to microbiologists. For example, unlike most other pathogenic spirochetes, the leptospiral OM is rich in lipopolysaccharide (LPS). Leptospiral LPS is similar to that of Gram-negative bacteria but has a number of unique structural features that may explain why it is not recognized by the LPS-specific Toll-like receptor 4 of humans. As in other spirochetes, lipoproteins are major components of the leptospiral OM, though their roles are poorly understood. The functions of transmembrane outer membrane proteins (OMPs) in many cases are better understood, thanks to homologies with their Gram-negative counterparts and the emergence of improved genetic techniques. This chapter will review recent discoveries involving the leptospiral OM and its role in leptospiral physiology and pathogenesis.
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Affiliation(s)
- David A Haake
- Division of Infectious Diseases, VA Greater Los Angeles Healthcare System, Los Angeles, CA, 90073, USA,
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Abstract
The mechanisms of disease pathogenesis in leptospirosis are poorly defined. Recent developments in the application of genetic tools in the study of Leptospira have advanced our understanding by allowing the assessment of mutants in animal models. As a result, a small number of essential virulence factors have been identified, though most do not have a clearly defined function. Significant advances have also been made in the in vitro characterization of leptospiral interaction with host structures, including extracellular matrix proteins (such as laminin, elastin, fibronectin, collagens), proteins related to hemostasis (fibrinogen, plasmin), and soluble mediators of complement resistance (factor H, C4b-binding protein), although none of these in vitro findings has been translated to the host animal. Binding to host structures may permit colonization of the host, prevention of blood clotting may contribute to hemorrhage, while interaction with complement resistance mediators may contribute to survival in serum. While not a classical intracellular pathogen, the interaction of leptospires and phagocytic cells appears complex, with bacteria surviving uptake and promoting apoptosis; mutants relating to these processes (such as cell invasion and oxidative stress resistance) are attenuated in vivo. Another feature of leptospiral biology is the high degree of functional redundancy and the surprising lack of attenuation of mutants in what appear to be certain virulence factors, such as LipL32 and LigB. While many advances have been made, there remains a lack of understanding of how Leptospira causes tissue pathology. It is likely that leptospires have many novel pathogenesis mechanisms that are yet to be identified.
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Abstract
Recent advances in molecular genetics, such as the ability to construct defined mutants, have allowed the study of virulence factors and more generally the biology in Leptospira. However, pathogenic leptospires remain much less easily transformable than the saprophyte L. biflexa and further development and improvement of genetic tools are required. Here, we review tools that have been used to genetically manipulate Leptospira. We also describe the major advances achieved in both genomics and postgenomics technologies, including transcriptomics and proteomics.
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Proteogenomic analysis and global discovery of posttranslational modifications in prokaryotes. Proc Natl Acad Sci U S A 2014; 111:E5633-42. [PMID: 25512518 DOI: 10.1073/pnas.1412722111] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We describe an integrated workflow for proteogenomic analysis and global profiling of posttranslational modifications (PTMs) in prokaryotes and use the model cyanobacterium Synechococcus sp. PCC 7002 (hereafter Synechococcus 7002) as a test case. We found more than 20 different kinds of PTMs, and a holistic view of PTM events in this organism grown under different conditions was obtained without specific enrichment strategies. Among 3,186 predicted protein-coding genes, 2,938 gene products (>92%) were identified. We also identified 118 previously unidentified proteins and corrected 38 predicted gene-coding regions in the Synechococcus 7002 genome. This systematic analysis not only provides comprehensive information on protein profiles and the diversity of PTMs in Synechococcus 7002 but also provides some insights into photosynthetic pathways in cyanobacteria. The entire proteogenomics pipeline is applicable to any sequenced prokaryotic organism, and we suggest that it should become a standard part of genome annotation projects.
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Witchell TD, Eshghi A, Nally JE, Hof R, Boulanger MJ, Wunder EA, Ko AI, Haake DA, Cameron CE. Post-translational modification of LipL32 during Leptospira interrogans infection. PLoS Negl Trop Dis 2014; 8:e3280. [PMID: 25356675 PMCID: PMC4214626 DOI: 10.1371/journal.pntd.0003280] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2014] [Accepted: 09/19/2014] [Indexed: 01/08/2023] Open
Abstract
Background Leptospirosis, a re-emerging disease of global importance caused by pathogenic Leptospira spp., is considered the world's most widespread zoonotic disease. Rats serve as asymptomatic carriers of pathogenic Leptospira and are critical for disease spread. In such reservoir hosts, leptospires colonize the kidney, are shed in the urine, persist in fresh water and gain access to a new mammalian host through breaches in the skin. Methodology/Principal Findings Previous studies have provided evidence for post-translational modification (PTM) of leptospiral proteins. In the current study, we used proteomic analyses to determine the presence of PTMs on the highly abundant leptospiral protein, LipL32, from rat urine-isolated L. interrogans serovar Copenhageni compared to in vitro-grown organisms. We observed either acetylation or tri-methylation of lysine residues within multiple LipL32 peptides, including peptides corresponding to regions of LipL32 previously identified as epitopes. Intriguingly, the PTMs were unique to the LipL32 peptides originating from in vivo relative to in vitro grown leptospires. The identity of each modified lysine residue was confirmed by fragmentation pattern analysis of the peptide mass spectra. A synthetic peptide containing an identified tri-methylated lysine, which corresponds to a previously identified LipL32 epitope, demonstrated significantly reduced immunoreactivity with serum collected from leptospirosis patients compared to the peptide version lacking the tri-methylation. Further, a subset of the identified PTMs are in close proximity to the established calcium-binding and putative collagen-binding sites that have been identified within LipL32. Conclusions/Significance The exclusive detection of PTMs on lysine residues within LipL32 from in vivo-isolated L. interrogans implies that infection-generated modification of leptospiral proteins may have a biologically relevant function during the course of infection. Although definitive determination of the role of these PTMs must await further investigations, the reduced immune recognition of a modified LipL32 epitope suggests the intriguing possibility that LipL32 modification represents a novel mechanism of immune evasion within Leptospira. Leptospirosis, caused by pathogenic Leptospira spp., constitutes an increasing global public health threat. Humans are accidental hosts, and acquire the disease primarily from contact with water sources that have been contaminated with urine from infected animals. Rats are asymptomatic carriers of infection and are critical for disease transmission to humans, particularly in urban slum environments. In this study, investigation of Leptospira directly isolated from the urine of infected rats showed acetylation or tri-methylation of the highly abundant leptospiral lipoprotein, LipL32. In comparison, Leptospira grown in culture did not result in any LipL32 lysine modifications. A synthetic peptide derived from LipL32 that incorporated a tri-methylated lysine modification exhibited less reactivity with serum from leptospirosis patients compared to an unmodified version of the peptide, suggesting LipL32 modifications may alter protein recognition by the immune response. This study reports, for the first time, modification of a Leptospira protein during infection, and suggests these modifications may have a functional consequence that contributes to bacterial persistence during infection.
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Affiliation(s)
- Timothy D. Witchell
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Azad Eshghi
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Jarlath E. Nally
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin, Ireland
| | - Rebecca Hof
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Martin J. Boulanger
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Elsio A. Wunder
- Department of Epidemiology of Microbial Disease, Yale School of Public Health, New Haven, Connecticut, United States of America
- Gonçalo Moniz Research Center, Oswaldo Cruz Foundation, Brazilian Ministry of Health, Salvador, Brazil
| | - Albert I. Ko
- Department of Epidemiology of Microbial Disease, Yale School of Public Health, New Haven, Connecticut, United States of America
- Gonçalo Moniz Research Center, Oswaldo Cruz Foundation, Brazilian Ministry of Health, Salvador, Brazil
| | - David A. Haake
- Division of Infectious Diseases, Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, California, United States of America
- Department of Medicine, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, California, United States of America
| | - Caroline E. Cameron
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
- * E-mail:
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Huang L, Zhu W, He P, Zhang Y, Zhuang X, Zhao G, Guo X, Qin J, Zhu Y. Re-characterization of an extrachromosomal circular plasmid in the pathogenic Leptospira interrogans serovar Lai strain 56601. Acta Biochim Biophys Sin (Shanghai) 2014; 46:605-11. [PMID: 24874103 DOI: 10.1093/abbs/gmu033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
In China, Leptospira interrogans serovar Lai strain 56601 (str.56601) is one of main pathogenic strains that cause severe leptospirosis in both human and animals. The genome of this organism was completely sequenced in 2003. However, in 2011, we identified and corrected some assembly errors in the str.56601 genome due to the repeat sequences widely distributed in the Leptospira genome. In this study, we re-analyzed the previously reported mobile, phage-related genomic island in the chromosome and rectified detailed sequence information in both the plasmid and chromosome using various experimental methods. The presence of a separate circular extrachromosomal plasmid was also confirmed, and its location in the genomic region was determined relative to the genomic island reported in L. interrogans serovar Lai by a combination of pulsed-field gel electrophoresis -based and plasmid extraction-based Southern blot analysis. This report confirmed that the separate extrachromosomal circular plasmid is not integrated into the chromosome of L. interrogans str.56601 and markedly improved our understanding of the genomic organization, evolution, and pathogenesis of L. interrogans. In particular, characterization of this extrachromosomal circular plasmid will contribute to the development of genetic manipulation systems in pathogenic Leptospira species.
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Affiliation(s)
- Lili Huang
- Department of Microbiology and Immunology, Institute of Medical Science, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, China
| | - Weinan Zhu
- Department of Microbiology and Immunology, Institute of Medical Science, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, China
| | - Ping He
- Department of Microbiology and Immunology, Institute of Medical Science, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, China
| | - Yan Zhang
- Department of Microbiology and Immunology, Institute of Medical Science, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, China
| | - Xuran Zhuang
- Department of Microbiology and Immunology, Institute of Medical Science, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, China
| | - Guoping Zhao
- CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xiaokui Guo
- Department of Microbiology and Immunology, Institute of Medical Science, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, China
| | - Jinhong Qin
- Department of Microbiology and Immunology, Institute of Medical Science, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, China
| | - Yongzhang Zhu
- Department of Microbiology and Immunology, Institute of Medical Science, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, China
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Characterisation of the Proteome of Leptospira interrogans Serovar Canicola as a Resource for the Identification of Common Serovar Immunogenic Proteins. INTERNATIONAL JOURNAL OF PROTEOMICS 2014; 2014:572901. [PMID: 24987528 PMCID: PMC4058600 DOI: 10.1155/2014/572901] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Revised: 04/24/2014] [Accepted: 04/24/2014] [Indexed: 11/18/2022]
Abstract
Over 230 serovars of Leptospira interrogans have been identified; however few have been completely characterised. The aim of this study was to characterise the proteome of serovar Canicola and to compare this against the serovars of Copenhageni and Pomona. 2D-LC/MS analysis identified 1653 Leptospira proteins in serovar Canicola; 60 of these proteins were common to Copenhageni and Pomona, 16 of which are known to be immunogenic. This study provides the first reported proteome for serovar Canicola and suggests that proteomic comparison of different serovars could be used as a tool for identification of novel target molecules for vaccine development.
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Lanouette S, Mongeon V, Figeys D, Couture JF. The functional diversity of protein lysine methylation. Mol Syst Biol 2014; 10:724. [PMID: 24714364 PMCID: PMC4023394 DOI: 10.1002/msb.134974] [Citation(s) in RCA: 177] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Large‐scale characterization of post‐translational modifications (PTMs), such as phosphorylation, acetylation and ubiquitination, has highlighted their importance in the regulation of a myriad of signaling events. While high‐throughput technologies have tremendously helped cataloguing the proteins modified by these PTMs, the identification of lysine‐methylated proteins, a PTM involving the transfer of one, two or three methyl groups to the ε‐amine of a lysine side chain, has lagged behind. While the initial findings were focused on the methylation of histone proteins, several studies have recently identified novel non‐histone lysine‐methylated proteins. This review provides a compilation of all lysine methylation sites reported to date. We also present key examples showing the impact of lysine methylation and discuss the circuitries wired by this important PTM.
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Affiliation(s)
- Sylvain Lanouette
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
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Cain JA, Solis N, Cordwell SJ. Beyond gene expression: the impact of protein post-translational modifications in bacteria. J Proteomics 2013; 97:265-86. [PMID: 23994099 DOI: 10.1016/j.jprot.2013.08.012] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 07/08/2013] [Accepted: 08/10/2013] [Indexed: 12/12/2022]
Abstract
The post-translational modification (PTM) of proteins plays a critical role in the regulation of a broad range of cellular processes in eukaryotes. Yet their role in governing similar systems in the conventionally presumed 'simpler' forms of life has been largely neglected and, until recently, was thought to occur only rarely, with some modifications assumed to be limited to higher organisms alone. Recent developments in mass spectrometry-based proteomics have provided an unparalleled power to enrich, identify and quantify peptides with PTMs. Additional modifications to biological molecules such as lipids and carbohydrates that are essential for bacterial pathophysiology have only recently been detected on proteins. Here we review bacterial protein PTMs, focusing on phosphorylation, acetylation, proteolytic degradation, methylation and lipidation and the roles they play in bacterial adaptation - thus highlighting the importance of proteomic techniques in a field that is only just in its infancy. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.
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Affiliation(s)
- Joel A Cain
- School of Molecular Bioscience, School of Medical Sciences, The University of Sydney, 2006, Australia
| | - Nestor Solis
- School of Molecular Bioscience, School of Medical Sciences, The University of Sydney, 2006, Australia
| | - Stuart J Cordwell
- School of Molecular Bioscience, School of Medical Sciences, The University of Sydney, 2006, Australia; Discipline of Pathology, School of Medical Sciences, The University of Sydney, 2006, Australia.
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Zeng L, Zhang Y, Zhu Y, Yin H, Zhuang X, Zhu W, Guo X, Qin J. Extracellular proteome analysis of Leptospira interrogans serovar Lai. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2013; 17:527-35. [PMID: 23895271 DOI: 10.1089/omi.2013.0043] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Abstract Leptospirosis is one of the most important zoonoses. Leptospira interrogans serovar Lai is a pathogenic spirochete that is responsible for leptospirosis. Extracellular proteins play an important role in the pathogenicity of this bacterium. In this study, L. interrogans serovar Lai was grown in protein-free medium; the supernatant was collected and subsequently analyzed as the extracellular proteome. A total of 66 proteins with more than two unique peptides were detected by MS/MS, and 33 of these were predicted to be extracellular proteins by a combination of bioinformatics analyses, including Psortb, cello, SoSuiGramN and SignalP. Comparisons of the transcriptional levels of these 33 genes between in vivo and in vitro conditions revealed that 15 genes were upregulated and two genes were downregulated in vivo compared to in vitro. A BLAST search for the components of secretion system at the genomic and proteomic levels revealed the presence of the complete type I secretion system and type II secretion system in this strain. Moreover, this strain also exhibits complete Sec translocase and Tat translocase systems. The extracellular proteome analysis of L. interrogans will supplement the previously generated whole proteome data and provide more information for studying the functions of specific proteins in the infection process and for selecting candidate molecules for vaccines or diagnostic tools for leptospirosis.
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Affiliation(s)
- Lingbing Zeng
- 1 Department of Medical Microbiology and Parasitology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine , Shanghai, China
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Pinne M, Haake DA. LipL32 Is a Subsurface Lipoprotein of Leptospira interrogans: presentation of new data and reevaluation of previous studies. PLoS One 2013; 8:e51025. [PMID: 23323152 PMCID: PMC3544172 DOI: 10.1371/journal.pone.0051025] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2012] [Accepted: 10/29/2012] [Indexed: 11/19/2022] Open
Abstract
The agents of leptospirosis, a zoonosis with worldwide distribution, are pathogenic spirochetes belonging to the genus Leptospira. The leptospiral life cycle involves transmission via fresh water and colonization of the renal tubules of their reservoir hosts. Infection of accidental hosts, including humans, may result in life-threatening sequelae. Bacterial outer membrane proteins (OMPs), particularly those with surface-exposed regions, play crucial roles in pathogen virulence mechanisms and adaptation to environmental conditions, including those found in the mammalian host. Therefore, elucidation and characterization of the surface-exposed OMPs of Leptospira spp. is of great interest in the leptospirosis field. A thorough, multi-pronged approach for assessing surface exposure of leptospiral OMPs is essential. Herein, we present evidence for a sub-surface location for most or all of the major leptospiral lipoprotein, LipL32, based on surface immunofluorescence utilizing three different types of antibodies and four different permeabilization methods, as well as surface proteolysis of intact and lysed leptospires. We reevaluate prior evidence presented in support of LipL32 surface-exposure and present a novel perspective on a protein whose location has been misleading researchers, due in large part to its extraordinary abundance in leptospiral cells.
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Affiliation(s)
- Marija Pinne
- Research Service, Veterans Affairs Greater Los Angeles Healthcare System, Los
Angeles, California, United States of America
- Department of Medicine, David Geffen School of Medicine, University of California
Los Angeles, Los Angeles, California, United States of America
- * E-mail:
| | - David A. Haake
- Division of Infectious Diseases, Veterans Affairs Greater Los Angeles Healthcare
System, Los Angeles, California, United States of America
- Department of Medicine, David Geffen School of Medicine, University of California
Los Angeles, Los Angeles, California, United States of America
- Department of Urology, David Geffen School of Medicine, University of California
Los Angeles, Los Angeles, California, United States of America
- Department of Microbiology, Immunology & Molecular Genetics, University of
California Los Angeles, Los Angeles, California, United States of America
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Murray GL, Lo M, Bulach DM, Srikram A, Seemann T, Quinsey NS, Sermswan RW, Allen A, Adler B. Evaluation of 238 antigens of Leptospira borgpetersenii serovar Hardjo for protection against kidney colonisation. Vaccine 2012. [PMID: 23176980 DOI: 10.1016/j.vaccine.2012.11.028] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Leptospirosis is a zoonotic disease affecting animals and humans worldwide. Leptospiral infection in cattle can cause reproductive failure and reduced weight gain, and importantly, infection represents a significant disease risk for farmers. Current bacterin vaccines offer protection that is short-lived and restricted at best to related serovars. The development of protective vaccines that stimulate immunity across multiple leptospiral serovars would therefore be advantageous. This study used a reverse vaccinology approach to evaluate a set of Leptospira borgpetersenii proteins in the hamster infection model. The L. borgpetersenii serovar Hardjo strain L550 genome sequence was analysed and genes encoding 262 predicted outer membrane or secreted proteins were selected. From this list, 238 proteins or protein fragments were successfully expressed and purified; 28 proteins (12%) were soluble, while the remaining 210 proteins (88%) were insoluble and purified under denaturing conditions. Proteins were mixed into 48 pools of up to five each and tested for protection against infection as assessed by renal colonisation in the hamster model of infection. None of the pools of antigens protected the hamsters against infection, despite a detectable antibody response being mounted against the majority of proteins (71%). This study is the first large scale evaluation of individual leptospiral proteins for ability to induce a protective immune response in the hamster infection model. It thus constitutes an important reference of protein immunogenicity and non-protective antigens that should be consulted before embarking on any future subunit vaccine experiments.
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Affiliation(s)
- Gerald L Murray
- Australian Research Council Centre of Excellence in Structural and Functional Microbial Genomics, Departments of Microbiology and Biochemistry & Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
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Srivastava R, Ray S, Vaibhav V, Gollapalli K, Jhaveri T, Taur S, Dhali S, Gogtay N, Thatte U, Srikanth R, Srivastava S. Serum profiling of leptospirosis patients to investigate proteomic alterations. J Proteomics 2012; 76 Spec No.:56-68. [PMID: 22554907 PMCID: PMC7185557 DOI: 10.1016/j.jprot.2012.04.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Revised: 03/20/2012] [Accepted: 04/07/2012] [Indexed: 11/05/2022]
Abstract
Leptospirosis is a zoonotic infectious disease of tropical, subtropical and temperate zones, which is caused by the pathogenic spirochetes of genus Leptospira. Although this zoonosis is generally not considered as fatal, the pathogen can eventually cause severe infection with septic shock, multi-organ failure and lethal pulmonary hemorrhages leading to mortality. In this study, we have performed a proteomic analysis of serum samples from leptospirosis patients (n = 6), febrile controls (falciparum malaria) (n = 8) and healthy subjects (n = 18) to obtain an insight about disease pathogenesis and host immune responses in leptospiral infections. 2DE and 2D-DIGE analysis in combination with MALDI-TOF/TOF MS revealed differential expression of 22 serum proteins in leptospirosis patients compared to the healthy controls. Among the identified differentially expressed proteins, 8 candidates exhibited different trends compared to the febrile controls. Functional analysis suggested the involvement of differentially expressed proteins in vital physiological pathways, including acute phase response, complement and coagulation cascades and hemostasis. This is the first report of analysis of human serum proteome alterations in leptospirosis patients, which revealed several differentially expressed proteins, including α-1-antitrypsin, vitronectin, ceruloplasmin, G-protein signaling regulator, apolipoprotein A-IV, which have not been reported in context of leptospirosis previously. This study will enhance our understanding about leptospirosis pathogenesis and provide a glimpse of host immunological responses. Additionally, a few differentially expressed proteins identified in this study may further be investigated as diagnostic or prognostic serum biomarkers for leptospirosis. This article is part of a Special Issue entitled: Integrated omics.
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Affiliation(s)
- Rajneesh Srivastava
- Wadhwani Research Center for Biosciences and Bioengineering, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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Weisbrod CR, Eng JK, Hoopmann MR, Baker T, Bruce JE. Accurate peptide fragment mass analysis: multiplexed peptide identification and quantification. J Proteome Res 2012; 11:1621-32. [PMID: 22288382 DOI: 10.1021/pr2008175] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fourier transform-all reaction monitoring (FT-ARM) is a novel approach for the identification and quantification of peptides that relies upon the selectivity of high mass accuracy data and the specificity of peptide fragmentation patterns. An FT-ARM experiment involves continuous, data-independent, high mass accuracy MS/MS acquisition spanning a defined m/z range. Custom software was developed to search peptides against the multiplexed fragmentation spectra by comparing theoretical or empirical fragment ions against every fragmentation spectrum across the entire acquisition. A dot product score is calculated against each spectrum to generate a score chromatogram used for both identification and quantification. Chromatographic elution profile characteristics are not used to cluster precursor peptide signals to their respective fragment ions. FT-ARM identifications are demonstrated to be complementary to conventional data-dependent shotgun analysis, especially in cases where the data-dependent method fails because of fragmenting multiple overlapping precursors. The sensitivity, robustness, and specificity of FT-ARM quantification are shown to be analogous to selected reaction monitoring-based peptide quantification with the added benefit of minimal assay development. Thus, FT-ARM is demonstrated to be a novel and complementary data acquisition, identification, and quantification method for the large scale analysis of peptides.
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Affiliation(s)
- Chad R Weisbrod
- Department of Genome Sciences, University of Washington , 815 Mercer Street, Seattle, Washington 98109, United States
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Jiang C. Translational medicine in China I: perspectives from Chinese physicians and scientists. SCIENCE CHINA-LIFE SCIENCES 2012; 54:1071-3. [PMID: 22227895 PMCID: PMC7099172 DOI: 10.1007/s11427-011-4260-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/20/2011] [Indexed: 12/11/2022]
Affiliation(s)
- ChengYu Jiang
- Department of Biochemistry and Molecular Biology, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100005 China
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Eshghi A, Pinne M, Haake DA, Zuerner RL, Frank A, Cameron CE. Methylation and in vivo expression of the surface-exposed Leptospira interrogans outer-membrane protein OmpL32. MICROBIOLOGY-SGM 2011; 158:622-635. [PMID: 22174381 DOI: 10.1099/mic.0.054767-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Recent studies have revealed that bacterial protein methylation is a widespread post-translational modification that is required for virulence in selected pathogenic bacteria. In particular, altered methylation of outer-membrane proteins has been shown to modulate the effectiveness of the host immune response. In this study, 2D gel electrophoresis combined with MALDI-TOF MS identified a Leptospira interrogans serovar Copenhageni strain Fiocruz L1-130 protein, corresponding to ORF LIC11848, which undergoes extensive and differential methylation of glutamic acid residues. Immunofluorescence microscopy implicated LIC11848 as a surface-exposed outer-membrane protein, prompting the designation OmpL32. Indirect immunofluorescence microscopy of golden Syrian hamster liver and kidney sections revealed expression of OmpL32 during colonization of these organs. Identification of methylated surface-exposed outer-membrane proteins, such as OmpL32, provides a foundation for delineating the role of this post-translational modification in leptospiral virulence.
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Affiliation(s)
- Azad Eshghi
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Marija Pinne
- Department of Medicine, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA, USA.,Research Service, 151, Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, CA, USA
| | - David A Haake
- Division of Infectious Diseases, 111F, Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, CA, USA.,Department of Medicine, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA, USA
| | - Richard L Zuerner
- Infectious Bacterial Diseases Research Unit, National Animal Disease Center (NADC), Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Ames, IA, USA
| | - Ami Frank
- Infectious Bacterial Diseases Research Unit, National Animal Disease Center (NADC), Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Ames, IA, USA
| | - Caroline E Cameron
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
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Identification of candidate host proteins that interact with LipL32, the major outer membrane protein of pathogenic Leptospira, by random phage display peptide library. Vet Microbiol 2011; 153:178-85. [DOI: 10.1016/j.vetmic.2011.04.030] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 04/05/2011] [Accepted: 04/18/2011] [Indexed: 11/23/2022]
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Figueira CP, Croda J, Choy HA, Haake DA, Reis MG, Ko AI, Picardeau M. Heterologous expression of pathogen-specific genes ligA and ligB in the saprophyte Leptospira biflexa confers enhanced adhesion to cultured cells and fibronectin. BMC Microbiol 2011; 11:129. [PMID: 21658265 PMCID: PMC3133549 DOI: 10.1186/1471-2180-11-129] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Accepted: 06/09/2011] [Indexed: 12/15/2022] Open
Abstract
Background In comparison to other bacterial pathogens, our knowledge of the molecular basis of the pathogenesis of leptospirosis is extremely limited. An improved understanding of leptospiral pathogenetic mechanisms requires reliable tools for functional genetic analysis. Leptospiral immunoglobulin-like (Lig) proteins are surface proteins found in pathogenic Leptospira, but not in saprophytes. Here, we describe a system for heterologous expression of the Leptospira interrogans genes ligA and ligB in the saprophyte Leptospira biflexa serovar Patoc. Results The genes encoding LigA and LigB under the control of a constitutive spirochaetal promoter were inserted into the L. biflexa replicative plasmid. We were able to demonstrate expression and surface localization of LigA and LigB in L. biflexa. We found that the expression of the lig genes significantly enhanced the ability of transformed L. biflexa to adhere in vitro to extracellular matrix components and cultured cells, suggesting the involvement of Lig proteins in cell adhesion. Conclusions This work reports a complete description of the system we have developed for heterologous expression of pathogen-specific proteins in the saprophytic L. biflexa. We show that expression of LigA and LigB proteins from the pathogen confers a virulence-associated phenotype on L. biflexa, namely adhesion to eukaryotic cells and fibronectin in vitro. This study indicates that L. biflexa can serve as a surrogate host to characterize the role of key virulence factors of the causative agent of leptospirosis.
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Comparative proteogenomic analysis of the Leptospira interrogans virulence-attenuated strain IPAV against the pathogenic strain 56601. Cell Res 2011; 21:1210-29. [PMID: 21423275 DOI: 10.1038/cr.2011.46] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
The virulence-attenuated Leptospira interrogans serovar Lai strain IPAV was derived by prolonged laboratory passage from a highly virulent ancestral strain isolated in China. We studied the genetic variations of IPAV that render it avirulent via comparative analysis against the pathogenic L. interrogans serovar Lai strain 56601. The complete genome sequence of the IPAV strain was determined and used to compare with, and then rectify and reannotate the genome sequence of strain 56601. Aside from their highly similar genomic structure and gene order, a total of 33 insertions, 53 deletions and 301 single-nucleotide variations (SNVs) were detected throughout the genome of IPAV directly affecting 101 genes, either in their 5' upstream region or within their coding region. Among them, the majority of the 44 functional genes are involved in signal transduction, stress response, transmembrane transport and nitrogen metabolism. Comparative proteomic analysis based on quantitative liquid chromatography (LC)-MS/MS data revealed that among 1 627 selected pairs of orthologs, 174 genes in the IPAV strain were upregulated, with enrichment mainly in classes of energy production and lipid metabolism. In contrast, 228 genes in strain 56601 were upregulated, with the majority enriched in the categories of protein translation and DNA replication/repair. The combination of genomic and proteomic approaches illustrated that altered expression or mutations in critical genes, such as those encoding a Ser/Thr kinase, carbon-starvation protein CstA, glutamine synthetase, GTP-binding protein BipA, ribonucleotide-diphosphate reductase and phosphate transporter, and alterations in the translational profile of lipoproteins or outer membrane proteins are likely to account for the virulence attenuation in strain IPAV.
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