Whole genome analyses for c-type cytochromes associated with respiratory chains in the extreme thermophile, Thermus thermophilus.

In thermophilic microorganisms, c-type cytochrome (cyt) proteins mainly function in the respiratory chain as electron carriers. Genome analyses at the beginning of this century revealed a variety of genes harboring the heme c motif. Here, we describe the results of surveying genes with the heme c motif, CxxCH, in a genome database comprising four strains of Thermus thermophilus, including strain HB8, and the confirmation of 19 c-type cytochromes among 27 selected genes. We analyzed the 19 genes, including the expression of four, by a bioinformatics approach to elucidate their individual attributes. One of the approaches included an analysis based on the secondary structure alignment pattern between the heme c motif and the 6th ligand. The predicted structures revealed many cyt c domains with fewer ß-strands, such as mitochondrial cyt c, in addition to the ß-strand unique to Thermus inserted in cyt c domains, as in T. thermophilus cyt c552 and caa3 cyt c oxidase subunit IIc. The surveyed thermophiles harbor potential proteins with a variety of cyt c folds. The gene analyses led to the development of an index for the classification of cyt c domains. Based on these results, we propose names for T. thermophilus genes harboring the cyt c fold.

A unique feature of hydrogen recovery in endogenous starch-to-alcohol fermentation of the marine microalga, Chlamydomonas perigranulata.

A unicellular marine green alga, Chlamydomonas perigranulata, was demonstrated to synthesize starch through photosynthesis, store it in a cell, and ferment it under anaerobic conditions in the dark to produce ethanol, 2,3-butanediol (butanediol), acetic acid, and carbon dioxide (CO2). Previous fermentation data of an algal biomass cultivated outdoors in a 50-L tubular photo-bioreactor showed good carbon (C) recovery in the fermentation balance, with a higher ratio to alcohols and, therefore, lower ratio to CO2 in the C distribution of products than what would be expected from the Embden-Myerhof-Parnas pathway. These findings led to a proposed concept for a CO2-ethanol conversion system (CDECS). The above data were evaluated in terms of hydrogen (H) recovery with the following results: C recovery at 105% was well balanced, although H recovery was as high as 139%, meaning an additional gain of H through fermentation. This finding was reproduced wholly in a set of experiments carried out in the same month of the following year, October, whereas another set of experiments was carried out in the following June provided ordinary fermentation results in terms of C and H recoveries with poor growth. Further analyses of these data revealed that butanediol is equal to ethanol as a product from a putative conversion system from CO2 to the detected fermentation products, leading to the revision of the CDECS concept to a CO2-alcohol conversion system (CDACS). The relevance of the CDACS will be discussed in relation to the cultivation conditions employed by chance.

A unique feature of hydrogen recovery in endogenous starch-to-alcohol fermentation of the marine microalga, Chlamydomonas perigranulata.

A unicellular marine green alga, Chlamydomonas perigranulata, was demonstrated to synthesize starch through photosynthesis, store it in a cell, and ferment it under anaerobic conditions in the dark to produce ethanol, 2,3-butanediol (butanediol), acetic acid, and carbon dioxide (CO2). Previous fermentation data of an algal biomass cultivated outdoors in a 50-L tubular photo-bioreactor showed good carbon (C) recovery in the fermentation balance, with a higher ratio to alcohols and, therefore, lower ratio to CO2 in the C distribution of products than what would be expected from the embden-Myerhof-Parnas pathway. These findings led to a proposed concept for a CO2-ethanol conversion system (CDECS). The above data were evaluated in terms of hydrogen (H) recovery with the following results: C recovery at 105% was well balanced, although H recovery was as high as 139%, meaning an additional gain of H through fermentation. This finding was reproduced wholly in a set of experiments carried out in the same month of the following year, October, whereas another set of experiments was carried out in the following June provided ordinary fermentation results in terms of C and H recoveries with poor growth. Further analyses of these data revealed that butanediol is equal to ethanol as a product from a putative conversion system from CO2 to the detected fermentation products, leading to the revision of the CDECS concept to a CO2-alcohol conversion system (CDACS). The relevance of the CDACS will be discussed in relation to the cultivation conditions employed by chance.

A novel Giraffidae-specific interspersed repeat with a microsatellite, originally found in an intron of a ruminant paralogous p97bcnt gene.

The ruminant-specific p97bcnt gene (bcntp97) is a paralogous gene that includes a region derived from a retrotransposable element 1 (RTE-1). The region comprises an exon (RTE-1 exon) encoding 325 amino acids in the middle of the p97bcnt protein. To understand how the bcntp97 paralog evolved, we examined its organization in several ruminants. We found a 700-base pair (bp) insert in the 5' intron of the RTE-1 exon in giraffe bcntp97. This insert is missing in the corresponding regions of bovine and sika deer. Furthermore, the sequence of the insert is interspersed in the genome of giraffe but not bovine and also contains a (GA)n microsatellite. A highly homologous insert harboring significantly different (GA)n microsatellite was detected in the corresponding region of okapi bcntp97. Therefore, the interspersed fragments with (GA)n microsatellite might serve as a marker for tracking how duplicated genes evolve in a family-specific manner.