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Annotation of Protein Domains Reveals Remarkable Conservation in the Functional Make up of Proteomes Across Superkingdoms.

Nasir A, Naeem A, Khan MJ, Nicora HD, Caetano-Anollés G - Genes (Basel) (2011)

Bottom Line: We finally identify few genomic outliers that deviate significantly from the conserved functional design.These include Nanoarchaeum equitans, proteobacterial symbionts of insects with extremely reduced genomes, Tenericutes and Guillardia theta.In turn, Protista and Bacteria shared similar functional distribution patterns suggesting an ancestral evolutionary link between these groups.

View Article: PubMed Central - PubMed

Affiliation: Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA. anasir@illinois.edu.

ABSTRACT
The functional repertoire of a cell is largely embodied in its proteome, the collection of proteins encoded in the genome of an organism. The molecular functions of proteins are the direct consequence of their structure and structure can be inferred from sequence using hidden Markov models of structural recognition. Here we analyze the functional annotation of protein domain structures in almost a thousand sequenced genomes, exploring the functional and structural diversity of proteomes. We find there is a remarkable conservation in the distribution of domains with respect to the molecular functions they perform in the three superkingdoms of life. In general, most of the protein repertoire is spent in functions related to metabolic processes but there are significant differences in the usage of domains for regulatory and extra-cellular processes both within and between superkingdoms. Our results support the hypotheses that the proteomes of superkingdom Eukarya evolved via genome expansion mechanisms that were directed towards innovating new domain architectures for regulatory and extra/intracellular process functions needed for example to maintain the integrity of multicellular structure or to interact with environmental biotic and abiotic factors (e.g., cell signaling and adhesion, immune responses, and toxin production). Proteomes of microbial superkingdoms Archaea and Bacteria retained fewer numbers of domains and maintained simple and smaller protein repertoires. Viruses appear to play an important role in the evolution of superkingdoms. We finally identify few genomic outliers that deviate significantly from the conserved functional design. These include Nanoarchaeum equitans, proteobacterial symbionts of insects with extremely reduced genomes, Tenericutes and Guillardia theta. These organisms spend most of their domains on information functions, including translation and transcription, rather than on metabolism and harbor a domain repertoire characteristic of parasitic organisms. In contrast, the functional repertoire of the proteomes of the Planctomycetes-Verrucomicrobia-Chlamydiae superphylum was no different than the rest of bacteria, failing to support claims of them representing a separate superkingdom. In turn, Protista and Bacteria shared similar functional distribution patterns suggesting an ancestral evolutionary link between these groups.

No MeSH data available.


Related in: MedlinePlus

The functional distribution of FSFs with respect to organism lifestyle. Both the percentage (A) and actual FSF numbers (B) indicate that obligate parasitic (OP) and facultative parasitic (P) organisms exhibit considerable variability in their metabolic repertoires (yellow trend lines) that is offset by corresponding increases in the Information FSFs (red trend lines).
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f3-genes-02-00869: The functional distribution of FSFs with respect to organism lifestyle. Both the percentage (A) and actual FSF numbers (B) indicate that obligate parasitic (OP) and facultative parasitic (P) organisms exhibit considerable variability in their metabolic repertoires (yellow trend lines) that is offset by corresponding increases in the Information FSFs (red trend lines).

Mentions: In order to explore whether organisms that engage in parasitic or symbiotic interactions have general tendencies that resemble those of the outliers, we classified organisms into three different lifestyles: free living (FL) (592 proteomes), facultative parasitic (P) (153 proteomes), and obligate parasitic (OP) (158 proteomes). Functional distributions for the seven general functional categories for these proteomic sets explained the role of parasitic life on proteomic constitution (Figure 3). Plots of percentages (Figure 3(A)) and actual number of FSFs in proteomes (Figure 3(B)) showed FSF distribution in FL organisms were remarkably homogenous and that the vast majority of variability within superkingdoms was ascribed to the P and OP lifestyles. This variability was for the most part explained by a sharp decline in the number of metabolic FSFs that are assigned to the Metabolism general category (Figure 3(B)). Plots also support the hypothesis that parasitic organisms have gone the route of massive genome reduction in a tendency to loose all of their metabolic genes. This tendency makes them more and more dependent on host cells for metabolic functions and survival [47,48].


Annotation of Protein Domains Reveals Remarkable Conservation in the Functional Make up of Proteomes Across Superkingdoms.

Nasir A, Naeem A, Khan MJ, Nicora HD, Caetano-Anollés G - Genes (Basel) (2011)

The functional distribution of FSFs with respect to organism lifestyle. Both the percentage (A) and actual FSF numbers (B) indicate that obligate parasitic (OP) and facultative parasitic (P) organisms exhibit considerable variability in their metabolic repertoires (yellow trend lines) that is offset by corresponding increases in the Information FSFs (red trend lines).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3927607&req=5

f3-genes-02-00869: The functional distribution of FSFs with respect to organism lifestyle. Both the percentage (A) and actual FSF numbers (B) indicate that obligate parasitic (OP) and facultative parasitic (P) organisms exhibit considerable variability in their metabolic repertoires (yellow trend lines) that is offset by corresponding increases in the Information FSFs (red trend lines).
Mentions: In order to explore whether organisms that engage in parasitic or symbiotic interactions have general tendencies that resemble those of the outliers, we classified organisms into three different lifestyles: free living (FL) (592 proteomes), facultative parasitic (P) (153 proteomes), and obligate parasitic (OP) (158 proteomes). Functional distributions for the seven general functional categories for these proteomic sets explained the role of parasitic life on proteomic constitution (Figure 3). Plots of percentages (Figure 3(A)) and actual number of FSFs in proteomes (Figure 3(B)) showed FSF distribution in FL organisms were remarkably homogenous and that the vast majority of variability within superkingdoms was ascribed to the P and OP lifestyles. This variability was for the most part explained by a sharp decline in the number of metabolic FSFs that are assigned to the Metabolism general category (Figure 3(B)). Plots also support the hypothesis that parasitic organisms have gone the route of massive genome reduction in a tendency to loose all of their metabolic genes. This tendency makes them more and more dependent on host cells for metabolic functions and survival [47,48].

Bottom Line: We finally identify few genomic outliers that deviate significantly from the conserved functional design.These include Nanoarchaeum equitans, proteobacterial symbionts of insects with extremely reduced genomes, Tenericutes and Guillardia theta.In turn, Protista and Bacteria shared similar functional distribution patterns suggesting an ancestral evolutionary link between these groups.

View Article: PubMed Central - PubMed

Affiliation: Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA. anasir@illinois.edu.

ABSTRACT
The functional repertoire of a cell is largely embodied in its proteome, the collection of proteins encoded in the genome of an organism. The molecular functions of proteins are the direct consequence of their structure and structure can be inferred from sequence using hidden Markov models of structural recognition. Here we analyze the functional annotation of protein domain structures in almost a thousand sequenced genomes, exploring the functional and structural diversity of proteomes. We find there is a remarkable conservation in the distribution of domains with respect to the molecular functions they perform in the three superkingdoms of life. In general, most of the protein repertoire is spent in functions related to metabolic processes but there are significant differences in the usage of domains for regulatory and extra-cellular processes both within and between superkingdoms. Our results support the hypotheses that the proteomes of superkingdom Eukarya evolved via genome expansion mechanisms that were directed towards innovating new domain architectures for regulatory and extra/intracellular process functions needed for example to maintain the integrity of multicellular structure or to interact with environmental biotic and abiotic factors (e.g., cell signaling and adhesion, immune responses, and toxin production). Proteomes of microbial superkingdoms Archaea and Bacteria retained fewer numbers of domains and maintained simple and smaller protein repertoires. Viruses appear to play an important role in the evolution of superkingdoms. We finally identify few genomic outliers that deviate significantly from the conserved functional design. These include Nanoarchaeum equitans, proteobacterial symbionts of insects with extremely reduced genomes, Tenericutes and Guillardia theta. These organisms spend most of their domains on information functions, including translation and transcription, rather than on metabolism and harbor a domain repertoire characteristic of parasitic organisms. In contrast, the functional repertoire of the proteomes of the Planctomycetes-Verrucomicrobia-Chlamydiae superphylum was no different than the rest of bacteria, failing to support claims of them representing a separate superkingdom. In turn, Protista and Bacteria shared similar functional distribution patterns suggesting an ancestral evolutionary link between these groups.

No MeSH data available.


Related in: MedlinePlus