TY  - JOUR
AU  - Gagić, Dragana
AU  - Ćirić, Milica
AU  - Wen, Wesley X.
AU  - Ng, Filomena
AU  - Rakonjac, Jasna
PY  - 2016
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/993
AB  - Microbial surface and secreted proteins (the secretome) contain a large number of proteins that interact with other microbes, host and/or environment. These proteins are exported by the coordinated activities of the protein secretion machinery present in the cell. A group of bacteriophage, called filamentous phage, have the ability to hijack bacterial protein secretion machinery in order to amplify and assemble via a secretion-like process. This ability has been harnessed in the use of filamentous phage of Escherichia coli in biotechnology applications, including screening large libraries of variants for binding to "bait" of interest, from tissues in vivo to pure proteins or even inorganic substrates. In this review we discuss the roles of secretome proteins in pathogenic and non-pathogenic bacteria and corresponding secretion pathways. We describe the basics of phage display technology and its variants applied to discovery of bacterial proteins that are implicated in colonization of host tissues and pathogenesis, as well as vaccine candidates through filamentous phage display library screening. Secretome selection aided by next-generation sequence analysis was successfully applied for selective display of the secretome at a microbial community scale, the latter revealing the richness of secretome functions of interest and surprising versatility in filamentous phage display of secretome proteins from large number of Gram-negative as well as Gram-positive bacteria and archaea.
PB  - Frontiers Media Sa, Lausanne
T2  - Frontiers in Microbiology
T1  - Exploring the Secretomes of Microbes and Microbial Communities Using Filamentous Phage Display
VL  - 7
DO  - 10.3389/fmicb.2016.00429
ER  - 

@article{
author = "Gagić, Dragana and Ćirić, Milica and Wen, Wesley X. and Ng, Filomena and Rakonjac, Jasna",
year = "2016",
abstract = "Microbial surface and secreted proteins (the secretome) contain a large number of proteins that interact with other microbes, host and/or environment. These proteins are exported by the coordinated activities of the protein secretion machinery present in the cell. A group of bacteriophage, called filamentous phage, have the ability to hijack bacterial protein secretion machinery in order to amplify and assemble via a secretion-like process. This ability has been harnessed in the use of filamentous phage of Escherichia coli in biotechnology applications, including screening large libraries of variants for binding to "bait" of interest, from tissues in vivo to pure proteins or even inorganic substrates. In this review we discuss the roles of secretome proteins in pathogenic and non-pathogenic bacteria and corresponding secretion pathways. We describe the basics of phage display technology and its variants applied to discovery of bacterial proteins that are implicated in colonization of host tissues and pathogenesis, as well as vaccine candidates through filamentous phage display library screening. Secretome selection aided by next-generation sequence analysis was successfully applied for selective display of the secretome at a microbial community scale, the latter revealing the richness of secretome functions of interest and surprising versatility in filamentous phage display of secretome proteins from large number of Gram-negative as well as Gram-positive bacteria and archaea.",
publisher = "Frontiers Media Sa, Lausanne",
journal = "Frontiers in Microbiology",
title = "Exploring the Secretomes of Microbes and Microbial Communities Using Filamentous Phage Display",
volume = "7",
doi = "10.3389/fmicb.2016.00429"
}

Gagić, D., Ćirić, M., Wen, W. X., Ng, F.,& Rakonjac, J.. (2016). Exploring the Secretomes of Microbes and Microbial Communities Using Filamentous Phage Display. in Frontiers in Microbiology
Frontiers Media Sa, Lausanne., 7.
https://doi.org/10.3389/fmicb.2016.00429

Gagić D, Ćirić M, Wen WX, Ng F, Rakonjac J. Exploring the Secretomes of Microbes and Microbial Communities Using Filamentous Phage Display. in Frontiers in Microbiology. 2016;7.
doi:10.3389/fmicb.2016.00429 .

Gagić, Dragana, Ćirić, Milica, Wen, Wesley X., Ng, Filomena, Rakonjac, Jasna, "Exploring the Secretomes of Microbes and Microbial Communities Using Filamentous Phage Display" in Frontiers in Microbiology, 7 (2016),
https://doi.org/10.3389/fmicb.2016.00429 . .

TY  - JOUR
AU  - Ćirić, Milica
AU  - Moon, Christina D.
AU  - Leahy, Sinead C.
AU  - Creevey, Christopher J.
AU  - Altermann, Eric
AU  - Attwood, Graeme T.
AU  - Rakonjac, Jasna
AU  - Gagić, Dragana
PY  - 2014
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/718
AB  - Background: In silico, secretome proteins can be predicted from completely sequenced genomes using various available algorithms that identify membrane-targeting sequences. For metasecretome (collection of surface, secreted and transmembrane proteins from environmental microbial communities) this approach is impractical, considering that the metasecretome open reading frames (ORFs) comprise only 10% to 30% of total metagenome, and are poorly represented in the dataset due to overall low coverage of metagenomic gene pool, even in large-scale projects. Results: By combining secretome-selective phage display and next-generation sequencing, we focused the sequence analysis of complex rumen microbial community on the metasecretome component of the metagenome. This approach achieved high enrichment (29 fold) of secreted fibrolytic enzymes from the plant-adherent microbial community of the bovine rumen. In particular, we identified hundreds of heretofore rare modules belonging to cellulosomes, cell-surface complexes specialised for recognition and degradation of the plant fibre. Conclusions: As a method, metasecretome phage display combined with next-generation sequencing has a power to sample the diversity of low-abundance surface and secreted proteins that would otherwise require exceptionally large metagenomic sequencing projects. As a resource, metasecretome display library backed by the dataset obtained by next-generation sequencing is ready for i) affinity selection by standard phage display methodology and ii) easy purification of displayed proteins as part of the virion for individual functional analysis.
PB  - BMC, London
T2  - BMC Genomics
T1  - Metasecretome-selective phage display approach for mining the functional potential of a rumen microbial community
VL  - 15
DO  - 10.1186/1471-2164-15-356
ER  - 

@article{
author = "Ćirić, Milica and Moon, Christina D. and Leahy, Sinead C. and Creevey, Christopher J. and Altermann, Eric and Attwood, Graeme T. and Rakonjac, Jasna and Gagić, Dragana",
year = "2014",
abstract = "Background: In silico, secretome proteins can be predicted from completely sequenced genomes using various available algorithms that identify membrane-targeting sequences. For metasecretome (collection of surface, secreted and transmembrane proteins from environmental microbial communities) this approach is impractical, considering that the metasecretome open reading frames (ORFs) comprise only 10% to 30% of total metagenome, and are poorly represented in the dataset due to overall low coverage of metagenomic gene pool, even in large-scale projects. Results: By combining secretome-selective phage display and next-generation sequencing, we focused the sequence analysis of complex rumen microbial community on the metasecretome component of the metagenome. This approach achieved high enrichment (29 fold) of secreted fibrolytic enzymes from the plant-adherent microbial community of the bovine rumen. In particular, we identified hundreds of heretofore rare modules belonging to cellulosomes, cell-surface complexes specialised for recognition and degradation of the plant fibre. Conclusions: As a method, metasecretome phage display combined with next-generation sequencing has a power to sample the diversity of low-abundance surface and secreted proteins that would otherwise require exceptionally large metagenomic sequencing projects. As a resource, metasecretome display library backed by the dataset obtained by next-generation sequencing is ready for i) affinity selection by standard phage display methodology and ii) easy purification of displayed proteins as part of the virion for individual functional analysis.",
publisher = "BMC, London",
journal = "BMC Genomics",
title = "Metasecretome-selective phage display approach for mining the functional potential of a rumen microbial community",
volume = "15",
doi = "10.1186/1471-2164-15-356"
}

Ćirić, M., Moon, C. D., Leahy, S. C., Creevey, C. J., Altermann, E., Attwood, G. T., Rakonjac, J.,& Gagić, D.. (2014). Metasecretome-selective phage display approach for mining the functional potential of a rumen microbial community. in BMC Genomics
BMC, London., 15.
https://doi.org/10.1186/1471-2164-15-356

Ćirić M, Moon CD, Leahy SC, Creevey CJ, Altermann E, Attwood GT, Rakonjac J, Gagić D. Metasecretome-selective phage display approach for mining the functional potential of a rumen microbial community. in BMC Genomics. 2014;15.
doi:10.1186/1471-2164-15-356 .

Ćirić, Milica, Moon, Christina D., Leahy, Sinead C., Creevey, Christopher J., Altermann, Eric, Attwood, Graeme T., Rakonjac, Jasna, Gagić, Dragana, "Metasecretome-selective phage display approach for mining the functional potential of a rumen microbial community" in BMC Genomics, 15 (2014),
https://doi.org/10.1186/1471-2164-15-356 . .

TY  - JOUR
AU  - Jovanović, Goran
AU  - Rakonjac, J
AU  - Model, P
PY  - 1999
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/119
AB  - Transcription of the phage-shock protein (psp) operon in Escherichia coli is driven by a sigma(54) promoter, stimulated by integration host factor and dependent on an upstream, cis-acting sequence and an activator protein, PspF. PspF belongs to the enhancer binding protein family but lacks an N-terminal regulatory domain. Purified PspF is not modified and has an ATPase activity that is increased twofold in the presence of DNA carrying the psp cis-acting sequence. Purified mutant I-Iis-tagged PspF that lacks the C-terminal DNA-binding motif has a DNA-independent ATPase activity when present at 30-fold the concentration of the wild-type protein. Both proteins oligomerize in solution in an ATP and DNA-independent manner. The wild-type activator protein, but not the DNA-binding mutant, binds specifically to the cis-acting sequence. Analysis of the sequence protected by PspF demonstrates the presence of two upstream binding sites within the sequence, UAS I and UAS II, which together constitute the psp enhancer. Protection at low protein concentrations is more pronounced and more extensive on a supercoiled DNA than on a linear template. Full expression of the psp operon upon hyperosmotic shock depends on wild-type PspF, but only partially requires the presence of the psp enhancer.
PB  - Academic Press Ltd- Elsevier Science Ltd, London
T2  - Journal of Molecular Biology
T1  - In vivo and in vitro activities of the Escherichia coli sigma(54) transcription activator, PspF, and its DNA-binding mutant, PspF Delta HTH
EP  - 483
IS  - 2
SP  - 469
VL  - 285
DO  - 10.1006/jmbi.1998.2263
ER  - 

@article{
author = "Jovanović, Goran and Rakonjac, J and Model, P",
year = "1999",
abstract = "Transcription of the phage-shock protein (psp) operon in Escherichia coli is driven by a sigma(54) promoter, stimulated by integration host factor and dependent on an upstream, cis-acting sequence and an activator protein, PspF. PspF belongs to the enhancer binding protein family but lacks an N-terminal regulatory domain. Purified PspF is not modified and has an ATPase activity that is increased twofold in the presence of DNA carrying the psp cis-acting sequence. Purified mutant I-Iis-tagged PspF that lacks the C-terminal DNA-binding motif has a DNA-independent ATPase activity when present at 30-fold the concentration of the wild-type protein. Both proteins oligomerize in solution in an ATP and DNA-independent manner. The wild-type activator protein, but not the DNA-binding mutant, binds specifically to the cis-acting sequence. Analysis of the sequence protected by PspF demonstrates the presence of two upstream binding sites within the sequence, UAS I and UAS II, which together constitute the psp enhancer. Protection at low protein concentrations is more pronounced and more extensive on a supercoiled DNA than on a linear template. Full expression of the psp operon upon hyperosmotic shock depends on wild-type PspF, but only partially requires the presence of the psp enhancer.",
publisher = "Academic Press Ltd- Elsevier Science Ltd, London",
journal = "Journal of Molecular Biology",
title = "In vivo and in vitro activities of the Escherichia coli sigma(54) transcription activator, PspF, and its DNA-binding mutant, PspF Delta HTH",
pages = "483-469",
number = "2",
volume = "285",
doi = "10.1006/jmbi.1998.2263"
}

Jovanović, G., Rakonjac, J.,& Model, P.. (1999). In vivo and in vitro activities of the Escherichia coli sigma(54) transcription activator, PspF, and its DNA-binding mutant, PspF Delta HTH. in Journal of Molecular Biology
Academic Press Ltd- Elsevier Science Ltd, London., 285(2), 469-483.
https://doi.org/10.1006/jmbi.1998.2263

Jovanović G, Rakonjac J, Model P. In vivo and in vitro activities of the Escherichia coli sigma(54) transcription activator, PspF, and its DNA-binding mutant, PspF Delta HTH. in Journal of Molecular Biology. 1999;285(2):469-483.
doi:10.1006/jmbi.1998.2263 .

Jovanović, Goran, Rakonjac, J, Model, P, "In vivo and in vitro activities of the Escherichia coli sigma(54) transcription activator, PspF, and its DNA-binding mutant, PspF Delta HTH" in Journal of Molecular Biology, 285, no. 2 (1999):469-483,
https://doi.org/10.1006/jmbi.1998.2263 . .

TY  - JOUR
AU  - Rakonjac, J
AU  - Jovanović, Goran
AU  - Model, P
PY  - 1997
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/106
AB  - We describe the use of transcriptional fusions to the phage shock protein (psp) promoter. These fusions are expressed only when cells are infected by filamentous phage. In an application, the psp promoter was fused to the protein coding part of filamentous phage gene III (gIII). Protein III (pIII) is needed to complement mutant fl phage containing a deletion of gIII but its synthesis also renders cells resistant to infection. By inducing pIII production from psp-gIII only in the cells that are already infected with phage, it was possible to obtain plaques from phage in which gill had been completely deleted. gIII was deleted from two helper phages: R408 and VCSM13, which were then propagated on cells containing the psp-gIII fusion. These two phages were tested for use in a phage display method that requires generation of noninfectious, phagemid-containing virion-like particles. Both helpers worked, but R408d3 was superior to VCSM13d3, because it generated about 1800-times fewer background infectious particles.
PB  - Elsevier Science Bv, Amsterdam
T2  - Gene
T1  - Filamentous phage infection-mediated gene expression: construction and propagation of the gIII deletion mutant helper phage R408d3
EP  - 103
IS  - 1-2
SP  - 99
VL  - 198
DO  - 10.1016/S0378-1119(97)00298-9
ER  - 

@article{
author = "Rakonjac, J and Jovanović, Goran and Model, P",
year = "1997",
abstract = "We describe the use of transcriptional fusions to the phage shock protein (psp) promoter. These fusions are expressed only when cells are infected by filamentous phage. In an application, the psp promoter was fused to the protein coding part of filamentous phage gene III (gIII). Protein III (pIII) is needed to complement mutant fl phage containing a deletion of gIII but its synthesis also renders cells resistant to infection. By inducing pIII production from psp-gIII only in the cells that are already infected with phage, it was possible to obtain plaques from phage in which gill had been completely deleted. gIII was deleted from two helper phages: R408 and VCSM13, which were then propagated on cells containing the psp-gIII fusion. These two phages were tested for use in a phage display method that requires generation of noninfectious, phagemid-containing virion-like particles. Both helpers worked, but R408d3 was superior to VCSM13d3, because it generated about 1800-times fewer background infectious particles.",
publisher = "Elsevier Science Bv, Amsterdam",
journal = "Gene",
title = "Filamentous phage infection-mediated gene expression: construction and propagation of the gIII deletion mutant helper phage R408d3",
pages = "103-99",
number = "1-2",
volume = "198",
doi = "10.1016/S0378-1119(97)00298-9"
}

Rakonjac, J., Jovanović, G.,& Model, P.. (1997). Filamentous phage infection-mediated gene expression: construction and propagation of the gIII deletion mutant helper phage R408d3. in Gene
Elsevier Science Bv, Amsterdam., 198(1-2), 99-103.
https://doi.org/10.1016/S0378-1119(97)00298-9

Rakonjac J, Jovanović G, Model P. Filamentous phage infection-mediated gene expression: construction and propagation of the gIII deletion mutant helper phage R408d3. in Gene. 1997;198(1-2):99-103.
doi:10.1016/S0378-1119(97)00298-9 .

Rakonjac, J, Jovanović, Goran, Model, P, "Filamentous phage infection-mediated gene expression: construction and propagation of the gIII deletion mutant helper phage R408d3" in Gene, 198, no. 1-2 (1997):99-103,
https://doi.org/10.1016/S0378-1119(97)00298-9 . .