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Article ; Online: The Plant-Associated Microbe Gene Ontology (PAMGO) Consortium

Collmer Candace W / Torto-Alalibo Trudy / Gwinn-Giglio Michelle

BMC Microbiology, Vol 9, Iss Suppl 1, p S

community development of new Gene Ontology terms describing biological processes involved in microbe-host interactions

2009 Volume 1

Abstract: Abstract All microbes that form beneficial, neutral, or pathogenic associations with hosts face similar challenges. They must physically adhere to and/or gain entry to host tissues; they must avoid, suppress, or tolerate host defenses; they must acquire ... ...

Abstract	Abstract All microbes that form beneficial, neutral, or pathogenic associations with hosts face similar challenges. They must physically adhere to and/or gain entry to host tissues; they must avoid, suppress, or tolerate host defenses; they must acquire nutrients from the host and successfully multiply. Microbes that associate with hosts come from many kingdoms of life and include bacteria, fungi, oomycetes, and nematodes. The increasing numbers of full genome sequences from these diverse microbes provide the opportunity to discover common mechanisms by which the microbes forge and maintain intimate associations with host organisms. However, cross-genome analyses have been hindered by lack of a universal vocabulary for describing biological processes involved in the interplay between microbes and their hosts. The Plant-Associated Microbe Gene Ontology (PAMGO) Consortium has been working for three years as an official interest group of the Gene Ontology (GO) Consortium to develop well-defined GO terms that describe many of the biological processes common to diverse plant- and animal-associated microbes. Creating these terms, over 700 at this time, has required a synthesis of diverse points of view from many research communities. The use of these terms in genome annotation will allow cross-genome searches for genes with common function (without demand for sequence similarity) and also improve the interpretation of data from high-throughput microarray and proteomic analyses. This article, and the more focused mini-reviews that make up this supplement to BMC Microbiology , describe the development and use of these terms.
Keywords	Microbiology ; QR1-502 ; Science ; Q ; DOAJ:Microbiology ; DOAJ:Biology ; DOAJ:Biology and Life Sciences
Subject code	501
Language	English
Publishing date	2009-02-01T00:00:00Z
Publisher	BioMed Central
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Genetic resources for methane production from biomass described with the Gene Ontology.

Purwantini, Endang / Torto-Alalibo, Trudy / Lomax, Jane / Setubal, João C / Tyler, Brett M / Mukhopadhyay, Biswarup

Frontiers in microbiology

2014 Volume 5, Page(s) 634

Abstract: Methane (CH4) is a valuable fuel, constituting 70-95% of natural gas, and a potent greenhouse gas. Release of CH4 into the atmosphere contributes to climate change. Biological CH4 production or methanogenesis is mostly performed by methanogens, a group ... ...

Abstract	Methane (CH4) is a valuable fuel, constituting 70-95% of natural gas, and a potent greenhouse gas. Release of CH4 into the atmosphere contributes to climate change. Biological CH4 production or methanogenesis is mostly performed by methanogens, a group of strictly anaerobic archaea. The direct substrates for methanogenesis are H2 plus CO2, acetate, formate, methylamines, methanol, methyl sulfides, and ethanol or a secondary alcohol plus CO2. In numerous anaerobic niches in nature, methanogenesis facilitates mineralization of complex biopolymers such as carbohydrates, lipids and proteins generated by primary producers. Thus, methanogens are critical players in the global carbon cycle. The same process is used in anaerobic treatment of municipal, industrial and agricultural wastes, reducing the biological pollutants in the wastes and generating methane. It also holds potential for commercial production of natural gas from renewable resources. This process operates in digestive systems of many animals, including cattle, and humans. In contrast, in deep-sea hydrothermal vents methanogenesis is a primary production process, allowing chemosynthesis of biomaterials from H2 plus CO2. In this report we present Gene Ontology (GO) terms that can be used to describe processes, functions and cellular components involved in methanogenic biodegradation and biosynthesis of specialized coenzymes that methanogens use. Some of these GO terms were previously available and the rest were generated in our Microbial Energy Gene Ontology (MENGO) project. A recently discovered non-canonical CH4 production process is also described. We have performed manual GO annotation of selected methanogenesis genes, based on experimental evidence, providing "gold standards" for machine annotation and automated discovery of methanogenesis genes or systems in diverse genomes. Most of the GO-related information presented in this report is available at the MENGO website (http://www.mengo.biochem.vt.edu/).
Language	English
Publishing date	2014-12-03
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2014.00634
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Genetic resources for advanced biofuel production described with the Gene Ontology.

Torto-Alalibo, Trudy / Purwantini, Endang / Lomax, Jane / Setubal, João C / Mukhopadhyay, Biswarup / Tyler, Brett M

Frontiers in microbiology

2014 Volume 5, Page(s) 528

Abstract: Dramatic increases in research in the area of microbial biofuel production coupled with high-throughput data generation on bioenergy-related microbes has led to a deluge of information in the scientific literature and in databases. Consolidating this ... ...

Abstract	Dramatic increases in research in the area of microbial biofuel production coupled with high-throughput data generation on bioenergy-related microbes has led to a deluge of information in the scientific literature and in databases. Consolidating this information and making it easily accessible requires a unified vocabulary. The Gene Ontology (GO) fulfills that requirement, as it is a well-developed structured vocabulary that describes the activities and locations of gene products in a consistent manner across all kingdoms of life. The Microbial ENergy processes Gene Ontology () project is extending the GO to include new terms to describe microbial processes of interest to bioenergy production. Our effort has added over 600 bioenergy related terms to the Gene Ontology. These terms will aid in the comprehensive annotation of gene products from diverse energy-related microbial genomes. An area of microbial energy research that has received a lot of attention is microbial production of advanced biofuels. These include alcohols such as butanol, isopropanol, isobutanol, and fuels derived from fatty acids, isoprenoids, and polyhydroxyalkanoates. These fuels are superior to first generation biofuels (ethanol and biodiesel esterified from vegetable oil or animal fat), can be generated from non-food feedstock sources, can be used as supplements or substitutes for gasoline, diesel and jet fuels, and can be stored and distributed using existing infrastructure. Here we review the roles of genes associated with synthesis of advanced biofuels, and at the same time introduce the use of the GO to describe the functions of these genes in a standardized way.
Language	English
Publishing date	2014-10-10
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2014.00528
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Article ; Online: Infection strategies of filamentous microbes described with the Gene Ontology.

Torto-Alalibo, Trudy / Meng, Shaowu / Dean, Ralph A

Trends in microbiology

2009 Volume 17, Issue 7, Page(s) 320–327

Abstract: Filamentous microbes that form highly developed symbiotic associations (ranging from pathogenesis to mutualism) with their hosts include fungi, oomycetes and actinomycete bacteria. These organisms share many common features in growth, development and ... ...

Abstract	Filamentous microbes that form highly developed symbiotic associations (ranging from pathogenesis to mutualism) with their hosts include fungi, oomycetes and actinomycete bacteria. These organisms share many common features in growth, development and infection and have evolved similar strategies for neutralizing host defense responses to establish symbioses. Recent advances in sequencing technologies have led to a remarkable increase in the number of sequenced genomes of filamentous organisms. Analysis of the available genomes has provided useful information about genes that might be important for host infection and colonization. However, because many functional similarities among these organisms have arisen by convergent evolution, sequence-based genomic comparisons will miss many genes that are functionally analogous. In the absence of sequence similarity, annotating genes with standardized terms from the Gene Ontology (GO) can facilitate functional comparisons. Here, we review common strategies employed by filamentous organisms during colonization of their hosts, with reference to GO terms that best describe the processes involved.
MeSH term(s)	Actinomycetales/genetics ; Computational Biology/methods ; Fungi/genetics ; Oomycetes/genetics ; Virulence Factors/genetics ; Virulence Factors/metabolism ; Vocabulary, Controlled
Chemical Substances	Virulence Factors
Language	English
Publishing date	2009-07
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
ZDB-ID	1158963-2
ISSN	1878-4380 ; 0966-842X
ISSN (online)	1878-4380
ISSN	0966-842X
DOI	10.1016/j.tim.2009.05.003
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Article ; Online: The Plant-Associated Microbe Gene Ontology (PAMGO) Consortium: community development of new Gene Ontology terms describing biological processes involved in microbe-host interactions.

Torto-Alalibo, Trudy / Collmer, Candace W / Gwinn-Giglio, Michelle

BMC microbiology

2009 Volume 9 Suppl 1, Page(s) S1

Abstract: All microbes that form beneficial, neutral, or pathogenic associations with hosts face similar challenges. They must physically adhere to and/or gain entry to host tissues; they must avoid, suppress, or tolerate host defenses; they must acquire nutrients ...

Abstract	All microbes that form beneficial, neutral, or pathogenic associations with hosts face similar challenges. They must physically adhere to and/or gain entry to host tissues; they must avoid, suppress, or tolerate host defenses; they must acquire nutrients from the host and successfully multiply. Microbes that associate with hosts come from many kingdoms of life and include bacteria, fungi, oomycetes, and nematodes. The increasing numbers of full genome sequences from these diverse microbes provide the opportunity to discover common mechanisms by which the microbes forge and maintain intimate associations with host organisms. However, cross-genome analyses have been hindered by lack of a universal vocabulary for describing biological processes involved in the interplay between microbes and their hosts. The Plant-Associated Microbe Gene Ontology (PAMGO) Consortium has been working for three years as an official interest group of the Gene Ontology (GO) Consortium to develop well-defined GO terms that describe many of the biological processes common to diverse plant- and animal-associated microbes. Creating these terms, over 700 at this time, has required a synthesis of diverse points of view from many research communities. The use of these terms in genome annotation will allow cross-genome searches for genes with common function (without demand for sequence similarity) and also improve the interpretation of data from high-throughput microarray and proteomic analyses. This article, and the more focused mini-reviews that make up this supplement to BMC Microbiology, describe the development and use of these terms.
MeSH term(s)	Bacteria/genetics ; Fungi/genetics ; Host-Pathogen Interactions ; Plants/microbiology ; Symbiosis/genetics ; Terminology as Topic ; Vocabulary, Controlled
Language	English
Publishing date	2009-02-19
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
ISSN	1471-2180
ISSN (online)	1471-2180
DOI	10.1186/1471-2180-9-S1-S1
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Common processes in pathogenesis by fungal and oomycete plant pathogens, described with Gene Ontology terms

Chibucos Marcus C / Torto-Alalibo Trudy / Meng Shaowu / Tyler Brett M / Dean Ralph A

BMC Microbiology, Vol 9, Iss Suppl 1, p S

2009 Volume 7

Abstract: Abstract Plant diseases caused by fungi and oomycetes result in significant economic losses every year. Although phylogenetically distant, the infection processes by these organisms share many common features. These include dispersal of an infectious ... ...

Abstract	Abstract Plant diseases caused by fungi and oomycetes result in significant economic losses every year. Although phylogenetically distant, the infection processes by these organisms share many common features. These include dispersal of an infectious particle, host adhesion, recognition, penetration, invasive growth, and lesion development. Previously, many of these common processes did not have corresponding Gene Ontology (GO) terms. For example, no GO terms existed to describe processes related to the appressorium, an important structure for infection by many fungi and oomycetes. In this mini-review, we identify common features of the pathogenic processes of fungi and oomycetes and create a pathogenesis model using 256 newly developed and 38 extant GO terms, with an emphasis on the appressorium and signal transduction. This set of standardized GO terms provides a solid base to further compare and contrast the molecular underpinnings of fungal and oomycete pathogenesis.
Keywords	Microbiology ; QR1-502 ; Science ; Q ; DOAJ:Microbiology ; DOAJ:Biology ; DOAJ:Biology and Life Sciences
Subject code	501
Language	English
Publishing date	2009-02-01T00:00:00Z
Publisher	BioMed Central
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Computational and comparative analyses of 150 full-length cDNA sequences from the oomycete plant pathogen Phytophthora infestans.

Win, Joe / Kanneganti, Thirumala-Devi / Torto-Alalibo, Trudy / Kamoun, Sophien

Fungal genetics and biology : FG & B

2006 Volume 43, Issue 1, Page(s) 20–33

Abstract: Phytophthora infestans is a devastating phytopathogenic oomycete that causes late blight on tomato and potato. Recent genome sequencing efforts of P. infestans and other Phytophthora species are generating vast amounts of sequence data providing ... ...

Abstract	Phytophthora infestans is a devastating phytopathogenic oomycete that causes late blight on tomato and potato. Recent genome sequencing efforts of P. infestans and other Phytophthora species are generating vast amounts of sequence data providing opportunities to unlock the complex nature of pathogenesis. However, accurate annotation of Phytophthora genomes will be a significant challenge. Most of the information about gene structure in these species was gathered from a handful of genes resulting in significant limitations for development of ab initio gene-calling programs. In this study, we collected a total of 150 bioinformatically determined near full-length cDNA (FLcDNA) sequences of P. infestans that were predicted to contain full open reading frame sequences. We performed detailed computational analyses of these FLcDNA sequences to obtain a snapshot of P. infestans gene structure, gauge the degree of sequence conservation between P. infestans genes and those of Phytophthora sojae and Phytophthora ramorum, and identify patterns of gene conservation between P. infestans and various eukaryotes, particularly fungi, for which genome-wide translated protein sequences are available. These analyses helped us to define the structural characteristics of P. infestans genes using a validated data set. We also determined the degree of sequence conservation within the genus Phytophthora and identified a set of fast evolving genes. Finally, we identified a set of genes that are shared between Phytophthora and fungal phytopathogens but absent in animal fungal pathogens. These results confirm that plant pathogenic oomycetes and fungi share virulence components, and suggest that eukaryotic microbial pathogens that share similar lifestyles also share a similar set of genes independently of their phylogenetic relatedness.
MeSH term(s)	Automatic Data Processing ; Base Composition ; DNA, Complementary/genetics ; DNA, Fungal/genetics ; Molecular Sequence Data ; Open Reading Frames/genetics ; Phytophthora/genetics ; Plant Diseases ; Sequence Analysis, DNA ; Solanaceae/microbiology
Chemical Substances	DNA, Complementary ; DNA, Fungal
Language	English
Publishing date	2006-01
Publishing country	United States
Document type	Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1319820-8
ISSN	1096-0937 ; 1087-1845 ; 0147-5975
ISSN (online)	1096-0937
ISSN	1087-1845 ; 0147-5975
DOI	10.1016/j.fgb.2005.10.003
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Zs.A 2431: Show issues

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Article ; Online: Common processes in pathogenesis by fungal and oomycete plant pathogens, described with Gene Ontology terms.

Meng, Shaowu / Torto-Alalibo, Trudy / Chibucos, Marcus C / Tyler, Brett M / Dean, Ralph A

BMC microbiology

2009 Volume 9 Suppl 1, Page(s) S7

Abstract: Plant diseases caused by fungi and oomycetes result in significant economic losses every year. Although phylogenetically distant, the infection processes by these organisms share many common features. These include dispersal of an infectious particle, ... ...

Abstract	Plant diseases caused by fungi and oomycetes result in significant economic losses every year. Although phylogenetically distant, the infection processes by these organisms share many common features. These include dispersal of an infectious particle, host adhesion, recognition, penetration, invasive growth, and lesion development. Previously, many of these common processes did not have corresponding Gene Ontology (GO) terms. For example, no GO terms existed to describe processes related to the appressorium, an important structure for infection by many fungi and oomycetes. In this mini-review, we identify common features of the pathogenic processes of fungi and oomycetes and create a pathogenesis model using 256 newly developed and 38 extant GO terms, with an emphasis on the appressorium and signal transduction. This set of standardized GO terms provides a solid base to further compare and contrast the molecular underpinnings of fungal and oomycete pathogenesis.
MeSH term(s)	Fungi/pathogenicity ; Host-Pathogen Interactions ; Oomycetes/pathogenicity ; Plant Diseases/microbiology ; Plants/microbiology ; Signal Transduction ; Spores/pathogenicity ; Terminology as Topic ; Vocabulary, Controlled
Language	English
Publishing date	2009-02-19
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
ISSN	1471-2180
ISSN (online)	1471-2180
DOI	10.1186/1471-2180-9-S1-S7
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Article ; Online: Common and contrasting themes in host cell-targeted effectors from bacterial, fungal, oomycete and nematode plant symbionts described using the Gene Ontology.

Torto-Alalibo, Trudy / Collmer, Candace W / Lindeberg, Magdalen / Bird, David / Collmer, Alan / Tyler, Brett M

BMC microbiology

2009 Volume 9 Suppl 1, Page(s) S3

Abstract: A wide diversity of plant-associated symbionts, including microbes, produce proteins that can enter host cells, or are injected into host cells in order to modify the physiology of the host to promote colonization. These molecules, termed effectors, ... ...

Abstract	A wide diversity of plant-associated symbionts, including microbes, produce proteins that can enter host cells, or are injected into host cells in order to modify the physiology of the host to promote colonization. These molecules, termed effectors, commonly target the host defense signaling pathways in order to suppress the defense response. Others target the gene expression machinery or trigger specific modifications to host morphology or physiology that promote the nutrition and proliferation of the symbiont. When recognized by the host's surveillance machinery, which includes cognate resistance (R) gene products, defense responses are engaged to restrict pathogen proliferation. Effectors from diverse symbionts may be delivered into plant cells via varied mechanisms, including whole organism cellular entry (viruses, some bacteria and fungi), type III and IV secretion (in bacteria), physical injection (nematodes and insects) and protein translocation signal sequences (oomycetes and fungi). This mini-review will summarize both similarities and differences in effectors and effector delivery systems found in diverse plant-associated symbionts as well as how these are described with Plant-Associated Microbe Gene Ontology (PAMGO) terms.
MeSH term(s)	Animals ; Bacteria/metabolism ; Biological Transport ; Fungi/metabolism ; Host-Pathogen Interactions ; Nematoda/metabolism ; Oomycetes/metabolism ; Plant Diseases/microbiology ; Plants/metabolism ; Plants/microbiology ; Symbiosis ; Terminology as Topic ; Vocabulary, Controlled
Language	English
Publishing date	2009-02-19
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
ISSN	1471-2180
ISSN (online)	1471-2180
DOI	10.1186/1471-2180-9-S1-S3
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Programmed cell death in host-symbiont associations, viewed through the Gene Ontology

Gwinn-Giglio Michelle / Torto-Alalibo Trudy / Collmer Candace W / Chibucos Marcus C / Lindeberg Magdalen / Li Donghui / Tyler Brett M

BMC Microbiology, Vol 9, Iss Suppl 1, p S

2009 Volume 5

Abstract: Abstract Manipulation of programmed cell death (PCD) is central to many host microbe interactions. Both plant and animal cells use PCD as a powerful weapon against biotrophic pathogens, including viruses, which draw their nutrition from living tissue. ... ...

Abstract	Abstract Manipulation of programmed cell death (PCD) is central to many host microbe interactions. Both plant and animal cells use PCD as a powerful weapon against biotrophic pathogens, including viruses, which draw their nutrition from living tissue. Thus, diverse biotrophic pathogens have evolved many mechanisms to suppress programmed cell death, and mutualistic and commensal microbes may employ similar mechanisms. Necrotrophic pathogens derive their nutrition from dead tissue, and many produce toxins specifically to trigger programmed cell death in their hosts. Hemibiotrophic pathogens manipulate PCD in a most exquisite way, suppressing PCD during the biotrophic phase and stimulating it during the necrotrophic phase. This mini-review will summarize the mechanisms that have evolved in diverse microbes and hosts for controlling PCD and the Gene Ontology terms developed by the Plant-Associated Microbe Gene Ontology (PAMGO) Consortium for describing those mechanisms.
Keywords	Microbiology ; QR1-502 ; Science ; Q ; DOAJ:Microbiology ; DOAJ:Biology ; DOAJ:Biology and Life Sciences
Subject code	501
Language	English
Publishing date	2009-02-01T00:00:00Z
Publisher	BioMed Central
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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