Hierarchical Clustering on RNA Dependent RNA Polymerase using Machine Learning.

RNA Dependent RNA Polymerase (RdRP) catalyzes the replication of RNA from an RNA template and is mostly found in Viruses. We have collected over 161 viral RdRP FASTA Sequences from the NCBI protein database using python script. Each of these sequences was transformed with TfidfVectorizer using sklearn module, with the one Letter word, because each Letter belongs to one Amino acid. These transformed data were sent to Hierarchical clustering using scipy library and visualized data using Dendrogram. These Machine Learning technique is able to classify or segment similar RdRp into one cluster. Each of these clusters was tested for their multiple sequence alignment with COBALT of NCBI. We observed that these clusters predicted similar RdRP among various viruses. These techniques can be further improved to segment or classify various proteins. These Machine Learning or Artificial Intelligence techniques need more improvement in their algorithms to solve genomics and proteomics.

Biochemical characterization and lysosomal localization of the mannose-6-phosphate protein p76 (hypothetical protein LOC196463)

Most soluble lysosomal proteins carry Man6P (mannose 6-phosphate), a specific carbohydrate marker that enables their binding to cellular MPRs (Man6P receptors) and their subsequent targeting towards the lysosome. This characteristic was exploited to identify novel soluble lysosomal proteins by proteomic analysis of Man6P proteins purified from a human cell line. Among the proteins identified during the course of the latter study [Journet, Chapel, Kieffer, Roux and Garin (2002) Proteomics, 2, 1026–1040], some had not been previously described as lysosomal proteins. We focused on a protein detected at 76 kDa by SDS/PAGE. We named this protein ‘p76’ and it appeared later in the NCBI protein database as the ‘hypothetical protein LOC196463’. In the present paper, we describe the identification of p76 by MS and we analyse several of its biochemical characteristics. The presence of Man6P sugars was confirmed by an MPR overlay experiment, which showed the direct and Man6P-dependent interaction between p76 and the MPR. The presence of six N-glycosylation sites was validated by progressive peptide-N-glycosidase F deglycosylation. Experiments using N- and C-termini directed anti-p76 antibodies provided insights into p76 maturation. Most importantly, we were able to demonstrate the lysosomal localization of this protein, which was initially suggested by its Man6P tags, by both immunofluorescence and sub-cellular fractionation of mouse liver homogenates.