1
|
Nielsen H. Protein Sorting Prediction. Methods Mol Biol 2024; 2715:27-63. [PMID: 37930519 DOI: 10.1007/978-1-0716-3445-5_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Many computational methods are available for predicting protein sorting in bacteria. When comparing them, it is important to know that they can be grouped into three fundamentally different approaches: signal-based, global property-based, and homology-based prediction. In this chapter, the strengths and drawbacks of each of these approaches are described through many examples of methods that predict secretion, integration into membranes, or subcellular locations in general. The aim of this chapter is to provide a user-level introduction to the field with a minimum of computational theory.
Collapse
Affiliation(s)
- Henrik Nielsen
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark.
| |
Collapse
|
2
|
Tancos MA, McMahon MB, Garrett WM, Luster DG, Rogers EE. Comparative Secretome Analyses of Toxigenic and Atoxigenic Rathayibacter Species. PHYTOPATHOLOGY 2021; 111:1530-1540. [PMID: 33499664 DOI: 10.1094/phyto-11-20-0495-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Phytopathogenic Rathayibacter species are unique bacterial plant pathogens because they are obligately vectored by plant parasitic anguinid nematodes to the developing seedheads of forage grasses and cereals. This understudied group of plant-associated Actinomycetes includes the neurotoxigenic plant pathogen R. toxicus, which causes annual ryegrass toxicity in grazing livestock. R. toxicus is currently endemic to Australia and is listed as a plant pathogen select agent by the U.S. Department of Agriculture-Animal and Plant Health Inspection Service. The complex Rathayibacter disease cycle requires intimate interactions with the nematode vector and plant hosts, which warrants an increased understanding of the secretory and surface-associated proteins that mediate these diverse eukaryotic interactions. Here we present the first comparative secretome analysis for this complex, nematode-vectored Rathayibacter genus that compares the three agronomically damaging toxigenic and atoxigenic Rathayibacter species, R. toxicus, R. iranicus, and R. tritici. The exoproteomic comparison identified 1,423 unique proteins between the three species via liquid chromatography-tandem mass spectrometry, leading to the identification of putative pathogenicity-related proteins and proteins that may mediate nematode attachment. Of the uniquely identified proteins, 94 homologous proteins were conserved between the three Rathayibacter exoproteomes and comprised between 43.4 and 58.6% of total protein abundance. Comparative analyses revealed both conserved and uniquely expressed extracellular proteins, which, interestingly, had more similarities to extracellular proteins commonly associated with bacterial animal pathogens than classic plant pathogens. This comparative exoproteome analysis will facilitate the characterization of proteins essential for vector attachment and host colonization and assist in the development of serological diagnostic assays.
Collapse
Affiliation(s)
- Matthew A Tancos
- Foreign Disease-Weed Science Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Frederick, MD
| | - Michael B McMahon
- Foreign Disease-Weed Science Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Frederick, MD
| | - Wesley M Garrett
- Animal Biosciences and Biotechnology Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD
| | - Douglas G Luster
- Foreign Disease-Weed Science Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Frederick, MD
| | - Elizabeth E Rogers
- Foreign Disease-Weed Science Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Frederick, MD
| |
Collapse
|
3
|
Wu H, Rebello O, Crost EH, Owen CD, Walpole S, Bennati-Granier C, Ndeh D, Monaco S, Hicks T, Colvile A, Urbanowicz PA, Walsh MA, Angulo J, Spencer DIR, Juge N. Fucosidases from the human gut symbiont Ruminococcus gnavus. Cell Mol Life Sci 2020; 78:675-693. [PMID: 32333083 PMCID: PMC7872956 DOI: 10.1007/s00018-020-03514-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 03/11/2020] [Accepted: 03/30/2020] [Indexed: 12/26/2022]
Abstract
The availability and repartition of fucosylated glycans within the gastrointestinal tract contributes to the adaptation of gut bacteria species to ecological niches. To access this source of nutrients, gut bacteria encode α-l-fucosidases (fucosidases) which catalyze the hydrolysis of terminal α-l-fucosidic linkages. We determined the substrate and linkage specificities of fucosidases from the human gut symbiont Ruminococcus gnavus. Sequence similarity network identified strain-specific fucosidases in R. gnavus ATCC 29149 and E1 strains that were further validated enzymatically against a range of defined oligosaccharides and glycoconjugates. Using a combination of glycan microarrays, mass spectrometry, isothermal titration calorimetry, crystallographic and saturation transfer difference NMR approaches, we identified a fucosidase with the capacity to recognize sialic acid-terminated fucosylated glycans (sialyl Lewis X/A epitopes) and hydrolyze α1–3/4 fucosyl linkages in these substrates without the need to remove sialic acid. Molecular dynamics simulation and docking showed that 3′-Sialyl Lewis X (sLeX) could be accommodated within the binding site of the enzyme. This specificity may contribute to the adaptation of R. gnavus strains to the infant and adult gut and has potential applications in diagnostic glycomic assays for diabetes and certain cancers.
Collapse
Affiliation(s)
- Haiyang Wu
- The Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Osmond Rebello
- Ludger Ltd, Culham Science Centre, Abingdon, OX14 3EB, UK
| | - Emmanuelle H Crost
- The Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - C David Owen
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK.,Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - Samuel Walpole
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Chloe Bennati-Granier
- The Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Didier Ndeh
- The Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Serena Monaco
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Thomas Hicks
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Anna Colvile
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK.,Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK.,The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | | | - Martin A Walsh
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK.,Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - Jesus Angulo
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.,Departamento de Química Orgánica, Universidad de Sevilla, C/ Prof. García González, 1, 41012, Sevilla, Spain.,Instituto de Investigaciones Químicas (CSIC-US), Avda. Américo Vespucio, 49, 41092, Sevilla, Spain
| | | | - Nathalie Juge
- The Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK.
| |
Collapse
|
4
|
Toshchakov SV, Lebedinsky AV, Sokolova TG, Zavarzina DG, Korzhenkov AA, Teplyuk AV, Chistyakova NI, Rusakov VS, Bonch-Osmolovskaya EA, Kublanov IV, Gavrilov SN. Genomic Insights Into Energy Metabolism of Carboxydocella thermautotrophica Coupling Hydrogenogenic CO Oxidation With the Reduction of Fe(III) Minerals. Front Microbiol 2018; 9:1759. [PMID: 30123201 PMCID: PMC6085454 DOI: 10.3389/fmicb.2018.01759] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Accepted: 07/13/2018] [Indexed: 01/17/2023] Open
Abstract
The genus Carboxydocella forms a deeply branching family in the class Clostridia and is currently represented by three physiologically diverse species of thermophilic prokaryotes. The type strain of the type species, Carboxydocella thermautotrophica 41T, is an obligate chemolithoautotroph growing exclusively by hydrogenogenic CO oxidation. Another strain, isolated from a hot spring at Uzon caldera, Kamchatka in the course of this work, is capable of coupling carboxydotrophy and dissimilatory reduction of Fe(III) from oxic and phyllosilicate minerals. The processes of carboxydotrophy and Fe(III) reduction appeared to be interdependent in this strain. The genomes of both isolates were sequenced, assembled into single chromosome sequences (for strain 41T a plasmid sequence was also assembled) and analyzed. Genome analysis revealed that each of the two strains possessed six genes encoding diverse Ni,Fe-containing CO dehydrogenases (maximum reported in complete prokaryotic genomes), indicating crucial role of carbon monoxide in C. thermautotrophica metabolism. Both strains possessed a set of 30 multiheme c-type cytochromes, but only the newly isolated Fe-reducing strain 019 had one extra gene of a 17-heme cytochrome, which is proposed to represent a novel determinant of dissimilatory iron reduction in prokaryotes. Mössbauer studies revealed that strain 019 induced reductive transformation of the abundant ferric/ferrous-mica mineral glauconite to siderite during carboxydotrophic growth. Reconstruction of the C. thermautotrophica strains energy metabolism is the first comprehensive genome analysis of a representative of the deep phylogenetic branch Clostridia Incertae Sedis, family V. Our data provide insights into energy metabolism of C. thermautotrophica with an emphasis on its ecological implications.
Collapse
Affiliation(s)
- Stepan V. Toshchakov
- Laboratory of Microbial Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander V. Lebedinsky
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Tatyana G. Sokolova
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Daria G. Zavarzina
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Alexei A. Korzhenkov
- Laboratory of Microbial Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Alina V. Teplyuk
- Laboratory of Microbial Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | | | | | | | - Ilya V. Kublanov
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Sergey N. Gavrilov
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
| |
Collapse
|
5
|
Nielsen H. Predicting Subcellular Localization of Proteins by Bioinformatic Algorithms. Curr Top Microbiol Immunol 2017; 404:129-158. [PMID: 26728066 DOI: 10.1007/82_2015_5006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
When predicting the subcellular localization of proteins from their amino acid sequences, there are basically three approaches: signal-based, global property-based, and homology-based. Each of these has its advantages and drawbacks, and it is important when comparing methods to know which approach was used. Various statistical and machine learning algorithms are used with all three approaches, and various measures and standards are employed when reporting the performances of the developed methods. This chapter presents a number of available methods for prediction of sorting signals and subcellular localization, but rather than providing a checklist of which predictors to use, it aims to function as a guide for critical assessment of prediction methods.
Collapse
Affiliation(s)
- Henrik Nielsen
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Kemitorvet building 208, 2800, Lyngby, Denmark.
| |
Collapse
|
6
|
Andreevskaya M, Johansson P, Jääskeläinen E, Rämö T, Ritari J, Paulin L, Björkroth J, Auvinen P. Lactobacillus oligofermentans glucose, ribose and xylose transcriptomes show higher similarity between glucose and xylose catabolism-induced responses in the early exponential growth phase. BMC Genomics 2016; 17:539. [PMID: 27487841 PMCID: PMC4972977 DOI: 10.1186/s12864-016-2840-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 06/15/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Lactobacillus oligofermentans has been mostly isolated from cold-stored packaged meat products in connection with their spoilage, but its precise role in meat spoilage is unknown. It belongs to the L. vaccinostercus group of obligate heterofermentative lactobacilli that generally ferment pentoses (e.g. xylose and ribose) more efficiently than hexoses (e.g. glucose). However, more efficient hexose utilization can be induced. The regulation mechanisms of the carbohydrate catabolism in such bacteria have been scarcely studied. To address this question, we provided the complete genome sequence of L. oligofermentans LMG 22743(T) and generated time course transcriptomes during its growth on glucose, ribose and xylose. RESULTS The genome was manually annotated and its main functional features were examined. L. oligofermentans was confirmed to be able to efficiently utilize several hexoses and maltose, which is, presumably, induced by its repeated cultivation with glucose in vitro. Unexpectedly, in the beginning of the exponential growth phase, glucose- and xylose-induced transcriptome responses were more similar, whereas toward the end of the growth phase xylose and ribose transcriptomes became more alike. The promoter regions of genes simultaneously upregulated both on glucose and xylose in comparison with ribose (particularly, hexose and xylose utilization genes) were found to be enriched in the CcpA- binding site. Transcriptionally, no glucose-induced carbon catabolite repression was detected. The catabolism of glucose, which requires initial oxidation, led to significant overexpression of the NAD(P)H re-oxidation genes, the upstream regions of which were found to contain a motif, which was highly similar to a Rex repressor binding site. CONCLUSIONS This paper presents the second complete genome and the first study of carbohydrate catabolism-dependent transcriptome response for a member of the L. vaccinostercus group. The transcriptomic changes detected in L. oligofermentans for growth with different carbohydrates differ significantly from those of facultative heterofermentative lactobacilli. The mechanism of CcpA regulation, putatively contributing to the observed similarities between glucose- and xylose-induced transcriptome responses and the absence of stringent carbon catabolite control, requires further studies. Finally, the cell redox balance maintenance, in terms of the NAD(P)+/NAD(P)H ratio, was predicted to be regulated by the Rex transcriptional regulator, supporting the previously made inference of Rex-regulons for members of the Lactobacillaceae family.
Collapse
Affiliation(s)
| | - Per Johansson
- Department of Food Hygiene and Environmental Health, University of Helsinki, Helsinki, Finland
| | - Elina Jääskeläinen
- Department of Food Hygiene and Environmental Health, University of Helsinki, Helsinki, Finland
| | - Tanja Rämö
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Present Address: The National Bureau of Investigation, Vantaa, Finland
| | - Jarmo Ritari
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Present Address: Finnish Red Cross Blood Service, Helsinki, Finland
| | - Lars Paulin
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Johanna Björkroth
- Department of Food Hygiene and Environmental Health, University of Helsinki, Helsinki, Finland
| | - Petri Auvinen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| |
Collapse
|
7
|
Chuzeville S, Dramsi S, Madec JY, Haenni M, Payot S. Antigen I/II encoded by integrative and conjugative elements of Streptococcus agalactiae and role in biofilm formation. Microb Pathog 2015; 88:1-9. [PMID: 26232503 DOI: 10.1016/j.micpath.2015.07.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 07/13/2015] [Accepted: 07/20/2015] [Indexed: 10/23/2022]
Abstract
Streptococcus agalactiae (i.e. Group B streptococcus, GBS) is a major human and animal pathogen. Genes encoding putative surface proteins and in particular an antigen I/II have been identified on Integrative and Conjugative Elements (ICEs) found in GBS. Antigens I/II are multimodal adhesins promoting colonization of the oral cavity by streptococci such as Streptococcus gordonii and Streptococcus mutans. The prevalence and diversity of antigens I/II in GBS were studied by a bioinformatic analysis. It revealed that antigens I/II, which are acquired by horizontal transfer via ICEs, exhibit diversity and are widespread in GBS, in particular in the serotype Ia/ST23 invasive strains. This study aimed at characterizing the impact on GBS biology of proteins encoded by a previously characterized ICE of S. agalactiae (ICE_515_tRNA(Lys)). The production and surface exposition of the antigen I/II encoded by this ICE was examined using RT-PCR and immunoblotting experiments. Surface proteins of ICE_515_tRNA(Lys) were found to contribute to GBS biofilm formation and to fibrinogen binding. Contribution of antigen I/II encoded by SAL_2056 to biofilm formation was also demonstrated. These results highlight the potential for ICEs to spread microbial adhesins between species.
Collapse
Affiliation(s)
- Sarah Chuzeville
- INRA, UMR1128 DynAMic, F-54506 Vandoeuvre-lès-Nancy, France; Université de Lorraine, UMR1128 DynAMic, F-54506 Vandoeuvre-lès-Nancy, France; ANSES Site de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Shaynoor Dramsi
- Institut Pasteur, Unité de Biologie des Bactéries Pathogènes à Gram-Positif, Paris, France; CNRS ERL3526, Paris, France
| | - Jean-Yves Madec
- ANSES Site de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Marisa Haenni
- ANSES Site de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Sophie Payot
- INRA, UMR1128 DynAMic, F-54506 Vandoeuvre-lès-Nancy, France; Université de Lorraine, UMR1128 DynAMic, F-54506 Vandoeuvre-lès-Nancy, France.
| |
Collapse
|
8
|
Miljkovic M, Strahinic I, Tolinacki M, Zivkovic M, Kojic S, Golic N, Kojic M. AggLb Is the Largest Cell-Aggregation Factor from Lactobacillus paracasei Subsp. paracasei BGNJ1-64, Functions in Collagen Adhesion, and Pathogen Exclusion In Vitro. PLoS One 2015; 10:e0126387. [PMID: 25955159 PMCID: PMC4425601 DOI: 10.1371/journal.pone.0126387] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 04/01/2015] [Indexed: 11/18/2022] Open
Abstract
Eleven Lactobacillus strains with strong aggregation abilities were selected from a laboratory collection. In two of the strains, genes associated with aggregation capability were plasmid located and found to strongly correlate with collagen binding. The gene encoding the auto-aggregation-promoting protein (AggLb) of Lactobacillus paracasei subsp. paracasei BGNJ1-64 was cloned using a novel, wide-range-host shuttle cloning vector, pAZILSJ. The clone pALb35, containing a 11377-bp DNA fragment, was selected from the SacI plasmid library for its ability to provide carriers with the aggregation phenotype. The complete fragment was sequenced and four potential ORFs were detected, including the aggLb gene and three surrounding transposase genes. AggLb is the largest known cell-surface protein in lactobacilli, consisting of 2998 aa (318,611 Da). AggLb belongs to the collagen-binding superfamily and its C-terminal region contains 20 successive repeats that are identical even at the nucleotide level. Deletion of aggLb causes a loss of the capacity to form cell aggregates, whereas overexpression increases cellular aggregation, hydrophobicity and collagen-binding potential. PCR screening performed with three sets of primers based on the aggLb gene of BGNJ1-64 enabled detection of the same type of aggLb gene in five of eleven selected aggregation-positive Lactobacillus strains. Heterologous expression of aggLb confirmed the crucial role of the AggLb protein in cell aggregation and specific collagen binding, indicating that AggLb has a useful probiotic function in effective colonization of host tissue and prevention of pathogen colonization.
Collapse
Affiliation(s)
- Marija Miljkovic
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444/a, P.O. Box 23, 11010, Belgrade, Serbia
| | - Ivana Strahinic
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444/a, P.O. Box 23, 11010, Belgrade, Serbia
| | - Maja Tolinacki
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444/a, P.O. Box 23, 11010, Belgrade, Serbia
| | - Milica Zivkovic
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444/a, P.O. Box 23, 11010, Belgrade, Serbia
| | - Snezana Kojic
- Laboratory for Molecular Biology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444/a, P.O. Box 23, 11010, Belgrade, Serbia
| | - Natasa Golic
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444/a, P.O. Box 23, 11010, Belgrade, Serbia
| | - Milan Kojic
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444/a, P.O. Box 23, 11010, Belgrade, Serbia
| |
Collapse
|