Thursday, 29th of April 2010 at 11:07:20 AM Metatranscriptomics reveals unique microbial small RNAs in the ocean’s water column
Yanmei Shi, et al., Nature
In the past weeks, the researcher use sequencing technique to reveal the environmental species’ information such as richness and functionality. The problem is not all the DNA sequences will be translated to the functional proteins. Some of the proteins might not to be the function under some situation, such as lack of enzyme, incorrect post-translation modification and so on. The information we cannot obtain directly from DNA sequence. Therefore, metaproteomics and metatranscriptomics are proposed to conquer these problems.
They perform RNA sequencing directly from natural microbial assemblages. Some previous studies report that they found some of the complementary DNA can’t find significant homology against with the current database. This indicates that some of the cDNA sequences might transcribe from uncharacterized proteins. The authors used four various data sets from the same location but distinct depth at Hawaii Ocean and found a large fraction of cDNA sequences can’t to be found in the coding region or even in ribosomal RNAs using homology search. That plentiful portion of cDNA sequences is classified as small RNAs and putative sRNAs..The sRNAs are a short piece of RNA, but it will not translate to protein, and usually we can be found then in the intergenic regions on the genomes.
They use a covariance-model-based algorithm to search all unassigned cDNA reads against with known sequence and structural similarity in Rfam. Then, the self-clustering approach is applied to all cDNA reads for better characterization of sRNA. Among found 66 groups, 9 groups were identified sRNA families in Rfam database and the rest groups were psRNA groups mapped to IGRs metagenomics fragments derived from marine planktonic microorganisms.
Finally, sRNAs are claimed to be the factor for controlling the gene expression in response to variable environmental conditions. Also, it is the first time they have some information about the correlation between metatranscriptomics and environment in RNA aspect. This method can be a good sensor for environment changing.
I have a little missing in this paper. They report so much biology information that I can’t fully understand. However, I think the address a very important issue that the environment absolutely can change the protein expression by the certain biology mechanisms.
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