Anaerolinea thermophila UNI-1T (= NBRC 100420T)
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Photo by Dr. Sekiguchi, National Institute of Advanced Industrial Science and Technology (AIST)
Members of the phylum Chloroflexi represent a wide variety of phenotypes, and distributed widely throughout the environment. The phylum Chloroflexi is currently divided into at least five classes based on 16S rRNA genes. Anaerolinea thermophila UNI-1T（= NBRC 100420T）belongs to the class Anaerolineae containing a number of diverse environmental 16S rRNA gene sequences with only a few cultured strains. A. thermophila UNI-1T is the first cultivated strain in this class.
A. thermophila UNI-1T was isolated from a thermophilic upflow anaerobic sludge blanket reactor treating fried soybean-curd manufacturing waste water. A. thermophila UNI-1T is a strictly anaerobic, filamentous (longer than 100 µm and 0.2 to 0.3 µm) bacterium that grows chemo-organotrophically on a number of carbohydrates and amino acids in the presence of yeast extract.
The genome of A. thermophila UNI-1T consisted of a single circular chromosome (3,532,378 bp; G+C content of 53.8%) containing 3,179 predicted protein-coding genes. The reconstructed central metabolic pathways from the A. thermophila UNI-1T genome showed that a lot of biosynthesis pathways whose products are essential for growth, such as nucleotide, methionine, fatty acid, vitamin and coenzyme seemed to be incomplete. Remarkably, the biosynthesis pathway of fatty acid seemed to lack genes necessary for the chain elongation. On the other hand, the genome encodes unique genes and pathways which have been mainly described for archaea. These analysis data would provide insights into the understanding of Anaerolineae species and their ecological environment.
Project history
2012-05-15 ..... 1
Release of proteome analysis result of Anaerolinea thermophila UNI-1T | We have analyzed the proteome of Anaerolinea thermophila UNI-1T by using the following method; 2D-PAGE followed by N-terminal amino acid sequencing.
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Summary of the genomic data
| Genomic size | 3,532,378 bp | ||||||||||||||||||||||||||||||||||||||||||||||||||
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| G+C content | 53.85 % | ||||||||||||||||||||||||||||||||||||||||||||||||||
| Number of ORFs assigned | 3,177 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| Percentage of the coding regions | 92.74 % | ||||||||||||||||||||||||||||||||||||||||||||||||||
| Percentage of the intronic regions | 0.00 % | ||||||||||||||||||||||||||||||||||||||||||||||||||
| Number of rRNA genes |
6
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| Number of tRNA genes |
50
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| Number of other features (misc_RNA,misc_feature,repeat) |
203
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General Procedure
The nucleotide sequence of the A. thermophila UNI-1T (= NBRC 100420T) genome was determined by the whole genome shotgun sequencing method as in the case of other organisms analyzed at NITE-DOB.
General Procedure
- DNA shotgun libraries
DNA shotgun libraries with inserts of 1.5, 2.0 and 5.0 kb in pUC118 vector (TaKaRa) was constructed.
- Fosmid library
A Fosmid library with inserts of 37 kb in the pCC1FOS fosmid vector was constructed using the CopyControl Fosmid Library Production Kit (Epicentre).
- Nucleotide sequencing
Plasmid and fosmid clones were end-sequenced using dye-terminator chemistry on an ABI 3730xl DNA Analyzer (ABI) or Base Station DNA Fragment Analyzer BST-0100 (MJ Research, Inc.). Sequence reads were trimmed at a threshold quality value of 20 by Phred and assembled by PHRAP/CONSED software (http://www.phrap.org).
- Gap closing
Gaps between the assembled sequences were closed by sequencing PCR products which bridge two neighboring contigs.
- Validation of the assembled sequence data
Contigs were compared according to their restriction pattern. Finally, each base of A. thermophila UNI-1 genome was ensured to be sequenced from multiple clones and from both directions with Phrap quality score ≧ 70 or from one direction with Phrap quality score ≧ 40.
Gene identification and annotation
- Putative non-translated genes were identified using the Rfam, tRNAscan-SE and ARAGORN programs.
- For the prediction of protein-coding genes, GLIMMER3 program was used. The initial set of ORFs was manually selected from the prediction result in combination with BLASTP.
- Similarity search results against Uniprot, Interpro and HAMAP database were used for functional prediction. The KEGG database was used for pathway reconstruction.
