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OwnerAlexei Slesarev, Andrei Malykh +3inventors
InventorsAlexei Slesarev, Andrei Malykh, Andrey Pavlov, Nadezhda Pavlova, Sergei Kozyavkin
Estimating the term…
We have determined the complete 1,694,969 nucleotide sequence of the GC-rich genome of Methanopyrus kandleri using a novel approach. It is based on unlinking genomic DNA with the ThermoFidelase version of M. kandleri topoisomerase V and cycle sequencing directed by 2′-modified oligonucleotides (Fimers). 3.3× sequencing redundancy was sufficient to assemble the genome with <1 error per 40 kb. Using a combination of sequence database searches and coding potential prediction, 1692 protein-coding genes and 39 genes for structural RNAs were identified. M. kandleri proteins show an unusually high content of negatively charged amino acids, which might be an adaptation to its high intracellular salinity. Previous phylogenetic analysis of 16S RNA suggested that M. kandleri belonged to a very deep branch, close to the root of the archaeal tree. However, genome comparisons, using both trees constructed from concatenated alignments of ribosomal proteins and trees based on gene content, indicate that M. kandleri consistently groups with other archaeal methanogens. M. kandleri shares the set of genes implicated in methanogenesis and, in part, its operon organization with Methanococcus jannaschii and Methanothermobacter thermoautotrophicus. These findings indicate that archaeal methanogens are monophyletic. A distinctive feature of M. kandleri is the paucity of proteins involved in signaling and regulation of gene expression: Also, M. kandleri appears to have fewer genes acquired via lateral transfer than other archaea. These features might reflect the extreme habitat of this organism.
An isolated nucleic acid encoding an M. kandleri protein as set forth in Schedule B.
An isolated polypeptide having an amino acid sequence at least 95% identical to the amino acid sequence selected from the group consisting of SEQ ID NOS 1-1688 and 1690-1692.
An isolated polypeptide having an amino acid sequence at least 85% identical to the amino acid sequence selected from the group consisting of SEQ ID NOS 1-1688 and 1690-1692.
An isolated nucleic acid molecule comprising a polynucleotide having a nucleotide sequence at least 95% identical to a sequence selected from the group consisting of:
A recombinant host cell capable of expressing the polypeptides identified in Schedule B.
Computer readable medium having recorded thereon the nucleotide sequence depicted in SEQ ID NO 1692 wherein the degree of said nucleotide identity is greater than at least 70%.
A method for identifying an amino acid sequence, comprising the step of searching for putative open reading frames or protein coding sequences within one or more of M. kandleri nucleotide sequences selected form the group consisting of SEQ ID NO 1693.
A method of producing a protein, comprising the step of expressing a protein comprising an amino acid sequence identified according to any one of claims 18-19.
A protein that is non-specifically stabilized by the presence of a protein identified by SEQ ID NOS 1-1688 and 1690-1692.
A method for improving the stability of a protein by introducing to said protein a polypeptide identified by at least one of said SEQ ID NOS 1-1688 and 1690-1692.
A method of increasing the enzymatic activity of a protein by introducing to said protein a polypeptide identified by at least one of said SEQ ID NOS 1-1688 and 1690-1692.
A method of increasing the structural activity of a protein by introducing to said protein a polypeptide identified by at least one of said SEQ ID NOS 1-1688 and 1690-1692.
A composition comprising a polypeptide identified by at least one of said SEQ ID NOS 1-1688 and 1690-1692 in combination with a protein not identified by one of said SEQ ID NOS 1-1688 and 1690-1692.
Dependencies are inferred from the claim text.