PSORTb v.2.0: Expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis

Gardy, Jennifer L.; Laird, Matthew R.; Chen, F.; Rey, Sébastien; Walsh, Calum J.; Ester, Martin; Brinkman, Fiona S. L.

doi:10.1093/bioinformatics/bti057

Cited by 671 publications

(568 citation statements)

References 18 publications

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“…In terms of annotation, a microbial genome analysis group would provide the community with results from the following analyses: putative ORFs searched against GenBank based on a pairwise sequence comparison method such as BLAST; HMMER2 (http://hmmer.wustl.edu/) used to search ORFs against the current collection of Pfam profile HMMs to locate regions that belong to known domain families; TopPred (25) used to identify membrane-spanning domains; SignalP (26) used to detect the presence of signal peptides and their likely cleavage sites; PSORT (27) used to predict the cellular location of proteins; transporters analyzed based on the classification schemes in TC-DB (http://tcdb.ucsd.edu/tcdb/); families of paralogous genes in a given genome constructed by pairwise searching of ORFs against themselves using BLASTP (matches with E≥10 6 over 60% of the query search length would be identified and clustered into multigene families); multiple alignments of protein families generated with CLUSTAL W (28); phylogenetic trees of genes and proteins built using PHYLIP (http://evolution.genetics. washington.edu/phylip.html).…”

Section: Annotation and Data Depositionmentioning

confidence: 99%

The Human Microbiome Project

Turnbaugh

Ley

Hamady

et al. 2007

Nature

4,962

3,417

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Our adult bodies harbor ~10 times more microbial than human cells. Their genomes (the microbiome) endow us with physiologic capacities that we have not had to evolve on our own and thus are both a manifestation of who we are genetically and metabolically, and a reflection of our state of well-being. Our distal gut is the highest density natural bacterial ecosystem known, the most comprehensively surveyed to date, and the most highly represented in pure culture. It contains more bacterial cells than all of our other microbial communities combined. To obtain a more comprehensive view of our biology, we propose a human gut microbiome initiative (HGMI) that will deliver deep draft whole genome sequences for 100 species representing the bacterial divisions (superkingdoms) known to comprise our distal gut microbiota: 15 of these genomes will be selected for finishing. A cost-effective strategy involves producing the bulk of the coverage by shotgun reads on a 454 Life Sciences pyrosequencer. Long-range linking information will be provided by paired end reads of fosmid subclones using a conventional ABI 3730xl capillary machine. The bulk of our sequencing will use human-derived strains, representing targeted phylotypes, from existing culture collections. The list will be augmented by in vivo culture of a human fecal microbiota in gnotobiotic mice. The latter approach will be used to obtain vastly simplified consortia, or pure cultures of previously uncultured representatives of important gutassociated bacteria. The deposited curated genome sequences will herald another phase of completion of the 'human' genome sequencing project, provide a key reference for metagenome projects, and serve as a model for future initiatives that seek to characterize our other extra-intestinal microbial communities.

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Section: Annotation and Data Depositionmentioning

confidence: 99%

The Human Microbiome Project

Turnbaugh

Ley

Hamady

et al. 2007

Nature

4,962

3,417

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“…As the shorter read length of pyrosequencing data affected the detection of protein localization, a comparison of each 0.1 mm 454 data set with the corresponding Sanger data set was performed. Using the assumption that percentage localizations calculated using PSORT (Gardy et al, 2005) should be the same between the two data sets, a correction factor was computed and applied. Genome size was inferred with GAAS (Angly et al, 2009) and the average number of rRNA operons was estimated by dividing the number of 16S rRNA genes detected in each sample by the average number of proteins assigned to COGs of 32 single-copy genes (COG0012, COG0016, COG0048, COG0049, COG0052, COG0080, COG0081, COG0087, COG0088, COG0090, COG0091, COG0092, COG0093, COG0094, COG0096, COG0097, COG0098, COG0099, COG0100, COG0102, COG0103, COG0124, COG0184, COG0185, COG0186, COG0197, COG0200, COG0201, COG0256, COG0522, COG0533 and COG0541).…”

Section: Read-based Analysesmentioning

confidence: 99%

An integrative study of a meromictic lake ecosystem in Antarctica

et al. 2010

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In nature, the complexity and structure of microbial communities varies widely, ranging from a few species to thousands of species, and from highly structured to highly unstructured communities. Here, we describe the identity and functional capacity of microbial populations within distinct layers of a pristine, marine-derived, meromictic (stratified) lake (Ace Lake) in Antarctica. Nine million open reading frames were analyzed, representing microbial samples taken from six depths of the lake size fractionated on sequential 3.0, 0.8 and 0.1 lm filters, and including metaproteome data from matching 0.1 lm filters. We determine how the interactions of members of this highly structured and moderately complex community define the biogeochemical fluxes throughout the entire lake. Our view is that the health of this delicate ecosystem is dictated by the effects of the polar light cycle on the dominant role of green sulfur bacteria in primary production and nutrient cycling, and the influence of viruses/phage and phage resistance on the cooperation between members of the microbial community right throughout the lake. To test our assertions, and develop a framework applicable to other microbially driven ecosystems, we developed a mathematical model that describes how cooperation within a microbial system is impacted by periodic fluctuations in environmental parameters on key populations of microorganisms. Our study reveals a mutualistic structure within the microbial community throughout the lake that has arisen as the result of mechanistic interactions between the physico-chemical parameters and the selection of individual members of the community. By exhaustively describing and modelling interactions in Ace Lake, we have developed an approach that may be applicable to learning how environmental perturbations affect the microbial dynamics in more complex aquatic systems.

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“…In silico analysis of the CC_2060 protein (PflI). Localization and general topology were determined based on the information from the pSORTb algorithm (17). The coiled-coil content was determined by the COILS program (29).…”

Section: Methodsmentioning

confidence: 99%

PflI, a Protein Involved in Flagellar Positioning in Caulobacter crescentus

Obuchowski

Jacobs‐Wagner

2008

J Bacteriol

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The bacterial flagellum is important for motility and adaptation to environmental niches. The sequence of events required for the synthesis of the flagellar apparatus has been extensively studied, yet the events that dictate where the flagellum is placed at the onset of flagellar biosynthesis remain largely unknown. We addressed this question for alphaproteobacteria by using the polarly flagellated alphaproteobacterium Caulobacter crescentus as an experimental model system. To identify candidates for a role in flagellar placement, we searched all available alphaproteobacterial genomes for genes of unknown function that cluster with early flagellar genes and that are present in polarly flagellated alphaproteobacteria while being absent in alphaproteobacteria with other flagellation patterns. From this in silico screen, we identified pflI. Loss of PflI function in C. crescentus results in an abnormally high frequency of cells with a randomly placed flagellum, while other aspects of cell polarization remain normal. In a wild-type background, a fusion of green fluorescent protein (GFP) and PflI localizes to the pole where the flagellum develops. This polar localization is independent of the flagellar protein FliF, whose oligomerization into the MS ring is thought to define the site of flagellar synthesis, suggesting that PflI acts before or independently of this event. Overproduction of PflI-GFP often leads to ectopic localization at the wrong, stalked pole. This is accompanied by a high frequency of flagellum formation at this ectopic site, suggesting that the location of PflI is a sufficient marker for a site for flagellar assembly.Flagellar arrangement has long been used as a defining characteristic in bacterial taxonomy. Bacteria can have flagella emerging from a specific site, such as the cell pole, or from seemingly random positions along the cell body (as in peritrichously flagellated bacteria). Differences in flagellar distribution can be important for how various species adapt to specific environments. While the biosynthesis of the flagellum and the temporal regulation of its assembly have been extensively studied (5, 32), we know little about what controls the cellular position of flagellar assembly. The distribution of flagella in peritrichous bacteria may be random and stochastically driven, but spatial mechanisms must exist in polarly flagellated bacteria to ensure that flagellar assembly takes place at the right location.It has been shown that in several polarly flagellated species of gammaproteobacteria, the flhF gene product is necessary for restricting the flagellum to a polar position (38, 41). flhF encodes a GTP-binding protein homologous to components of the signal recognition particle (SRP) pathway; in its absence, Pseudomonas putida and Pseudomonas aeruginosa have reduced motility and randomly placed flagella on the cell surface (25,38,41). Surprisingly, flhF homologs are also found in species with multiple, randomly placed flagella, indicating that FlhF is not a defining component of polarly f...

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PSORTb v.2.0: Expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis

Abstract: http://www.psort.org/psortb/supplementaryinfo.html.

Cited by 671 publications

References 18 publications

The Human Microbiome Project

The Human Microbiome Project

An integrative study of a meromictic lake ecosystem in Antarctica

PflI, a Protein Involved in Flagellar Positioning in Caulobacter crescentus

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