Mplexans Tetrahymena thermophila Genome Sequence Total Percent of ORFs , which could

Mplexans Tetrahymena thermophila Genome Sequence Total Percent of ORFs , which could assist in responding to sudden changes of the ionic environment. T. thermophila encodes six homologs of this adenylate cyclase/K transporter, whereas the parasitic apicomplexans P. falciparum and Cryptosporidium parvum encode only one each. The robust transporter systems present are likely a reflection of T. thermophila’s behavioral and physiological versatility as a free-living single-celled organism and its exposure to a wide range of different substrates in its natural environment. Entinostat custom synthesis Examination of the specific types of expansions suggests that functions associated with transport of K and other cations have been greatly diversified. Thus such functions may play a role in many of the unique aspects of the biology of this species and ciliates in general. Proteolytic processing. T. thermophila is a voracious predator and thus might be expected to have a wide diversity of proteolytic enzymes. Analysis of the predicted proteins in T. thermophila reveals some conflicting results relating to this idea. On the one hand, many of the largest clusters of lineagespecific duplications are of proteases. On the other hand, the total number of proteases identified is relatively low in terms of PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/19861045 the fraction of the proteome compared to other model organisms that have been sequenced and annotated. The conflict is most likely a reflection of the diversity of physiological processes in which proteases function. Thus we examined the subclassification of types of proteases present in more detail. Using the Merops protease nomenclature, which is based on intrinsic evolutionary and structural relationships the T. thermophila proteases were divided into five catalytic classes and 40 families. These are: 43 aspartic proteases belonging to two families, 211 cysteine proteases belonging to 11 families, 139 metalloproteases belonging to 14 families, 73 serine proteases belonging to 12 families, and 14 threonine proteases belonging to the T1 family. Some unique features of T. thermophila can be seen by comparison to P. falciparum which is the most closely related sequenced species to have a detailed analysis of its proteases published. Twenty-one protease families are present in both genomes. For example, the highly conserved threonine proteases and the ubiquitin carboxyl-terminal hydrolase families reflect the crucial role of the ATP-dependent ubiquitinproteasome system, which has been implicated in cell-cycle control and stress response. Nineteen protease families are present in T. thermophila but not P. falciparum. One of these includes leishmanolysin, originally identified in the kinetoplastid parasite Leishmania major and thought to be LGX818 involved in processing surface proteins. This family is greatly expanded in T. thermophila and suggests that surface protein processes may be important here, although the functions of leishmanolysin-related proteases in nonkinetoplastid eukaryotes remain unclear. In addition, some cytoskeletal protein types are apparently absent from T. thermophila; these include intermediate filament proteins as already suggested by biochemical studies, some microtubule-associated proteins and some actin-binding proteins. To better understand what role genes involved in microtubule and cytoskeletal functions might have played in the diversification of this species, we focused analysis on some of the genes with apparent expansions: tubulins, dyneins, and regulato.Mplexans Tetrahymena thermophila Genome Sequence Total Percent of ORFs , which could assist in responding to sudden changes of the ionic environment. T. thermophila encodes six homologs of this adenylate cyclase/K transporter, whereas the parasitic apicomplexans P. falciparum and Cryptosporidium parvum encode only one each. The robust transporter systems present are likely a reflection of T. thermophila’s behavioral and physiological versatility as a free-living single-celled organism and its exposure to a wide range of different substrates in its natural environment. Examination of the specific types of expansions suggests that functions associated with transport of K and other cations have been greatly diversified. Thus such functions may play a role in many of the unique aspects of the biology of this species and ciliates in general. Proteolytic processing. T. thermophila is a voracious predator and thus might be expected to have a wide diversity of proteolytic enzymes. Analysis of the predicted proteins in T. thermophila reveals some conflicting results relating to this idea. On the one hand, many of the largest clusters of lineagespecific duplications are of proteases. On the other hand, the total number of proteases identified is relatively low in terms of PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/19861045 the fraction of the proteome compared to other model organisms that have been sequenced and annotated. The conflict is most likely a reflection of the diversity of physiological processes in which proteases function. Thus we examined the subclassification of types of proteases present in more detail. Using the Merops protease nomenclature, which is based on intrinsic evolutionary and structural relationships the T. thermophila proteases were divided into five catalytic classes and 40 families. These are: 43 aspartic proteases belonging to two families, 211 cysteine proteases belonging to 11 families, 139 metalloproteases belonging to 14 families, 73 serine proteases belonging to 12 families, and 14 threonine proteases belonging to the T1 family. Some unique features of T. thermophila can be seen by comparison to P. falciparum which is the most closely related sequenced species to have a detailed analysis of its proteases published. Twenty-one protease families are present in both genomes. For example, the highly conserved threonine proteases and the ubiquitin carboxyl-terminal hydrolase families reflect the crucial role of the ATP-dependent ubiquitinproteasome system, which has been implicated in cell-cycle control and stress response. Nineteen protease families are present in T. thermophila but not P. falciparum. One of these includes leishmanolysin, originally identified in the kinetoplastid parasite Leishmania major and thought to be involved in processing surface proteins. This family is greatly expanded in T. thermophila and suggests that surface protein processes may be important here, although the functions of leishmanolysin-related proteases in nonkinetoplastid eukaryotes remain unclear. In addition, some cytoskeletal protein types are apparently absent from T. thermophila; these include intermediate filament proteins as already suggested by biochemical studies, some microtubule-associated proteins and some actin-binding proteins. To better understand what role genes involved in microtubule and cytoskeletal functions might have played in the diversification of this species, we focused analysis on some of the genes with apparent expansions: tubulins, dyneins, and regulato.