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Snapshot of the eukaryotic gene expression in muskoxen rumen--a metatranscriptomic approach.

Qi M, Wang P, O'Toole N, Barboza PS, Ungerfeld E, Leigh MB, Selinger LB, Butler G, Tsang A, McAllister TA, Forster RJ - PLoS ONE (2011)

Bottom Line: These included a number of glycoside hydrolase family 6 (GH6), GH48 and swollenin modules, which have rarely been described in previous gut metagenomic studies.The muskoxen rumen metatranscriptome demonstrates a much higher percentage of cellulase enzyme discovery and an 8.7x higher rate of total carbohydrate active enzyme discovery per gigabase of sequence than previous rumen metagenomes.This study provides a snapshot of eukaryotic gene expression in the muskoxen rumen, and identifies a number of candidate genes coding for potentially valuable lignocellulolytic enzymes.

View Article: PubMed Central - PubMed

Affiliation: Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada.

ABSTRACT

Background: Herbivores rely on digestive tract lignocellulolytic microorganisms, including bacteria, fungi and protozoa, to derive energy and carbon from plant cell wall polysaccharides. Culture independent metagenomic studies have been used to reveal the genetic content of the bacterial species within gut microbiomes. However, the nature of the genes encoded by eukaryotic protozoa and fungi within these environments has not been explored using metagenomic or metatranscriptomic approaches.

Methodology/principal findings: In this study, a metatranscriptomic approach was used to investigate the functional diversity of the eukaryotic microorganisms within the rumen of muskoxen (Ovibos moschatus), with a focus on plant cell wall degrading enzymes. Polyadenylated RNA (mRNA) was sequenced on the Illumina Genome Analyzer II system and 2.8 gigabases of sequences were obtained and 59129 contigs assembled. Plant cell wall degrading enzyme modules including glycoside hydrolases, carbohydrate esterases and polysaccharide lyases were identified from over 2500 contigs. These included a number of glycoside hydrolase family 6 (GH6), GH48 and swollenin modules, which have rarely been described in previous gut metagenomic studies.

Conclusions/significance: The muskoxen rumen metatranscriptome demonstrates a much higher percentage of cellulase enzyme discovery and an 8.7x higher rate of total carbohydrate active enzyme discovery per gigabase of sequence than previous rumen metagenomes. This study provides a snapshot of eukaryotic gene expression in the muskoxen rumen, and identifies a number of candidate genes coding for potentially valuable lignocellulolytic enzymes.

Show MeSH
Amino acid sequence similarities of carbohydrate active enzymes identified from the muskoxen rumen metatranscriptome (using all assembled contigs) versus top BLASTX match to the Genbank nr database.
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pone-0020521-g005: Amino acid sequence similarities of carbohydrate active enzymes identified from the muskoxen rumen metatranscriptome (using all assembled contigs) versus top BLASTX match to the Genbank nr database.

Mentions: To circumvent this problem, similar analyses were also performed on the assembled contigs. In total, we identified over 2500 contigs with a significant match to at least one CAZy module (Table S4). Since the use of short contigs may overestimate the total number of enzymes, we further restricted our targets to those contigs longer than 500 base pairs (1082 in total, Tables S4, S5, S6). These contigs, especially those assembled from larger numbers of reads, could serve as good candidates of potentially useful lignocellulolytic enzymes. Only 17% of these contigs were more than 70% identical to genes in the nr database, while 46% of them had less than 50% identity (Figure 5). Seventeen percent of the CAZy genes identified were most similar to nr database sequences annotated as “(Conserved) hypothetical protein”, “predicted protein” or “unnamed protein product”. These results indicated that rumen eukaryotes produce a large variety of glycoside hydrolases (GHs) with many of them remaining uncharacterized. There were 242 contigs that had two or more distinct CAZy domains. Carbohydrate binding domain (CBM) family 10/fungal dockerin domains were predominant in these multi domain enzymes, and were found in 190 (78.5%) of these contigs. Glycoside hydrolases from families GH6, GH45, and GH48 were found in 25, 25 and 23 multi-domain contigs respectively, most of which were linked to CBM10 modules.


Snapshot of the eukaryotic gene expression in muskoxen rumen--a metatranscriptomic approach.

Qi M, Wang P, O'Toole N, Barboza PS, Ungerfeld E, Leigh MB, Selinger LB, Butler G, Tsang A, McAllister TA, Forster RJ - PLoS ONE (2011)

Amino acid sequence similarities of carbohydrate active enzymes identified from the muskoxen rumen metatranscriptome (using all assembled contigs) versus top BLASTX match to the Genbank nr database.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3105075&req=5

pone-0020521-g005: Amino acid sequence similarities of carbohydrate active enzymes identified from the muskoxen rumen metatranscriptome (using all assembled contigs) versus top BLASTX match to the Genbank nr database.
Mentions: To circumvent this problem, similar analyses were also performed on the assembled contigs. In total, we identified over 2500 contigs with a significant match to at least one CAZy module (Table S4). Since the use of short contigs may overestimate the total number of enzymes, we further restricted our targets to those contigs longer than 500 base pairs (1082 in total, Tables S4, S5, S6). These contigs, especially those assembled from larger numbers of reads, could serve as good candidates of potentially useful lignocellulolytic enzymes. Only 17% of these contigs were more than 70% identical to genes in the nr database, while 46% of them had less than 50% identity (Figure 5). Seventeen percent of the CAZy genes identified were most similar to nr database sequences annotated as “(Conserved) hypothetical protein”, “predicted protein” or “unnamed protein product”. These results indicated that rumen eukaryotes produce a large variety of glycoside hydrolases (GHs) with many of them remaining uncharacterized. There were 242 contigs that had two or more distinct CAZy domains. Carbohydrate binding domain (CBM) family 10/fungal dockerin domains were predominant in these multi domain enzymes, and were found in 190 (78.5%) of these contigs. Glycoside hydrolases from families GH6, GH45, and GH48 were found in 25, 25 and 23 multi-domain contigs respectively, most of which were linked to CBM10 modules.

Bottom Line: These included a number of glycoside hydrolase family 6 (GH6), GH48 and swollenin modules, which have rarely been described in previous gut metagenomic studies.The muskoxen rumen metatranscriptome demonstrates a much higher percentage of cellulase enzyme discovery and an 8.7x higher rate of total carbohydrate active enzyme discovery per gigabase of sequence than previous rumen metagenomes.This study provides a snapshot of eukaryotic gene expression in the muskoxen rumen, and identifies a number of candidate genes coding for potentially valuable lignocellulolytic enzymes.

View Article: PubMed Central - PubMed

Affiliation: Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada.

ABSTRACT

Background: Herbivores rely on digestive tract lignocellulolytic microorganisms, including bacteria, fungi and protozoa, to derive energy and carbon from plant cell wall polysaccharides. Culture independent metagenomic studies have been used to reveal the genetic content of the bacterial species within gut microbiomes. However, the nature of the genes encoded by eukaryotic protozoa and fungi within these environments has not been explored using metagenomic or metatranscriptomic approaches.

Methodology/principal findings: In this study, a metatranscriptomic approach was used to investigate the functional diversity of the eukaryotic microorganisms within the rumen of muskoxen (Ovibos moschatus), with a focus on plant cell wall degrading enzymes. Polyadenylated RNA (mRNA) was sequenced on the Illumina Genome Analyzer II system and 2.8 gigabases of sequences were obtained and 59129 contigs assembled. Plant cell wall degrading enzyme modules including glycoside hydrolases, carbohydrate esterases and polysaccharide lyases were identified from over 2500 contigs. These included a number of glycoside hydrolase family 6 (GH6), GH48 and swollenin modules, which have rarely been described in previous gut metagenomic studies.

Conclusions/significance: The muskoxen rumen metatranscriptome demonstrates a much higher percentage of cellulase enzyme discovery and an 8.7x higher rate of total carbohydrate active enzyme discovery per gigabase of sequence than previous rumen metagenomes. This study provides a snapshot of eukaryotic gene expression in the muskoxen rumen, and identifies a number of candidate genes coding for potentially valuable lignocellulolytic enzymes.

Show MeSH