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Aspergillus oryzae RIB40
Saccharomyces cerevisiae K7
Aeropyrum pernix K1T
Sulfolobus tokodaii strain 7T
Methanocella paludicola SANAET
Pyrococcus horikoshii OT3T
Kitasatospora setae NBRC 14216T
Rhodococcus opacus B4
Rhodococcus erythropolis PR4
Kocuria rhizophila DC2201
Microlunatus phosphovorus NM-1T
Corynebacterium efficiens YS-314T
Streptomyces avermitilis MA-4680T
Caldisericum exile AZM16c01T
Anaerolinea thermophila UNI-1T
Arthrospira platensis NIES-39
Deferribacter desulfuricans SSM1T
Staphylococcus haemolyticus JCSC1435
Staphylococcus aureus MW2
Staphylococcus aureus N315
Brevibacillus brevis NBRC 100599
Oscillibacter valericigenes Sjm18-20T
Gemmatimonas aurantiaca T-27T
Acetobacter pasteurianus IFO 3283-32
Acidiphilium multivorum AIU301
Sphingobium japonicum UT26S
Sphingobium sp. SYK-6
Desulfovibrio magneticus RS-1
Salmonella enterica serovar Typhimurium T000240
About this genome
Comparative complete genome sequence analysis of the amino acid replacements responsible for the thermostability of
Nishio Y.,Nakamura Y.,Kawarabayasi Y.,Usuda Y.,Kimura E.,Sugimoto S.,Matsui K.,Yamagishi A.,Kikuchi H.,Ikeo K.,Gojobori T.
Genome Res. 13 (2003) 1572-9
Corynebacterium efficiens is the closest relative of Corynebacterium glutamicum, a species widely used for the industrial production of amino acids. C. efficiens but not C. glutamicum can grow above 40 degrees C. We sequenced the complete C. efficiens genome to investigate the basis of its thermostability by comparing its genome with that of C. glutamicum. The difference in GC content between the species was reflected in codon usage and nucleotide substitutions. Our comparative genomic study clearly showed that there was tremendous bias in amino acid substitutions in all orthologous ORFs. Analysis of the direction of the amino acid substitutions suggested that three substitutions are important for the stability of the C. efficiens proteins: from lysine to arginine, serine to alanine, and serine to threonine. Our results strongly suggest that the accumulation of these three types of amino acid substitutions correlates with the acquisition of thermostability and is responsible for the greater GC content of C. efficiens.
Evolutionary process of amino acid biosynthesis in
at the whole genome level.
Nishio Y.,Nakamura Y.,Usuda Y.,Sugimoto S.,Matsui K.,Kawarabayasi Y.,Kikuchi H.,Gojobori T.,Ikeo K.
Mol. Biol. Evol. 21 (2004) 1683-91
Corynebacterium glutamicum, which is the closest relative of Corynebacterium efficiens, is widely used for the large scale production of many kinds of amino acids, particularly glutamic acid and lysine, by fermentation. Corynebacterium diphtheriae, which is well known as a human pathogen, is also closely related to these two species of Corynebacteria, but it lacks such productivity of amino acids. It is an important and interesting question to ask how those closely related bacterial species have undergone such significant functional differentiation in amino acid biosynthesis. The main purpose of the present study is to clarify the evolutionary process of functional differentiation among the three species of Corynebacteria by conducting a comparative analysis of genome sequences. When Mycobacterium and Streptomyces were used as out groups, our comparative study suggested that the common ancestor of Corynebacteria already possessed almost all of the gene sets necessary for amino acid production. However, C. diphtheriae was found to have lost the genes responsible for amino acid production. Moreover, we found that the common ancestor of C. efficiens and C. glutamicum have acquired some of genes responsible for amino acid production by horizontal gene transfer. Thus, we conclude that the evolutionary events of gene loss and horizontal gene transfer must have been responsible for functional differentiation in amino acid biosynthesis of the three species of Corynebacteria.
The genome stability in
species due to lack of the recombinational repair system.
Nakamura Y.,Nishio Y.,Ikeo K.,Gojobori T.
Gene 317 (2003) 149-55
Corynebacterium species are members of gram-positive bacteria closely related to Mycobacterium species, both of which are classified into the same taxonomic order Actinomycetales. Recently, three corynebacteria, Corynebacterium efficiens, Corynebacterium glutamicum, and Corynebacterium diphtheriae have been sequenced independently. We found that the order of orthologous genes in these species has been highly conserved though it has been disrupted in Mycobacterium species. This synteny suggests that corynebacteria have rarely undergone extensive genome rearrangements and have maintained ancestral genome structures even after the divergence of corynebacteria and mycobacteria. This is the first report that the genome structures have been conserved in free-living bacteria such as C. efficiens and C. glutamicum, although it has been reported that obligate parasites such as Mycoplasma and Chlamydia have the stable genomes. The comparison of recombinational repair systems among the three corynebacteria and Mycobacterium tuberculosis suggested that the absence of recBCD genes in corynebacteria be responsible for the suppression of genome shuffling in the species. The genome stability in Corynebacterium species will give us hints of the speciation mechanism with the non-shuffled genome, particularly the importance of horizontal gene transfer and nucleotide substitution in the genome.
sp. nov., a glutamic-acid-producing species from soil and vegetables.
Fudou R.,Jojima Y.,Seto A.,Yamada K.,Kimura E.,Nakamatsu T.,Hiraishi A.,Yamanaka S.
Int. J. Syst. Evol. Microbiol. 52 (2002) 1127-31
Three glutamic-acid-producing coryneform strains were isolated from soil and vegetable samples. Chemotaxonomic investigations indicated that these strains belonged to the genus Corynebacterium. Phylogenetic studies, based on 16S rDNA analysis, demonstrated that the three strains formed a distinct cluster within the genus Corynebacterium and that their nearest relatives were Corynebacterium glutamicum and Corynebacterium callunae, also known as glutamic-acid-producing species. The data from 16S rDNA sequence and DNA-DNA relatedness studies clearly indicated that the three isolates represented a new species within the genus Corynebacterium. All of the isolates could grow at 45 degrees C and produced acid from dextrin; these were the most significant characteristics differentiating the three isolates from their neighbours. On the basis of the data presented here, it is proposed that the three glutamic-acid-producing isolates together be classified as Corynebacterium efficiens sp. nov., the type strain of which is YS-314T (= AJ 12310T = JCM 11189T = DSM 44549T).
National Institute of Technology and Evaluation
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