Protein length in eukaryotic and prokaryotic proteomes

We analyzed length differences of eukaryotic, bacterial and archaeal proteins in relation to function, conservation and environmental factors. Comparing Eukaryotes and Prokaryotes, we found that the greater length of eukaryotic proteins is pervasive over all functional categories and involves the vast majority of protein families. The magnitude of these differences suggests that the evolution of eukaryotic proteins was influenced by processes of fusion of single-function proteins into extended multi-functional and multi-domain proteins. Comparing Bacteria and Archaea, we determined that the small but significant length difference observed between their proteins results from a combination of three factors: (i) bacterial proteomes include a greater proportion than archaeal proteomes of longer proteins involved in metabolism or cellular processes, (ii) within most functional classes, protein families unique to Bacteria are generally longer than protein families unique to Archaea and (iii) within the same protein family, homologs from Bacteria tend to be longer than the corresponding homologs from Archaea. These differences are interpreted with respect to evolutionary trends and prevailing environmental conditions within the two prokaryotic groups

hsp70 genes in the human genome: Conservation and differentiation patterns predict a wide array of overlapping and specialized functions

<p>Abstract</p> <p>Background</p> <p>Hsp70 chaperones are required for key cellular processes and response to environmental changes and survival but they have not been fully characterized yet. The human <it>hsp70</it>-gene family has an unknown number of members (eleven counted over ten years ago); some have been described but the information is incomplete and inconsistent. A coherent body of knowledge encompassing all family components that would facilitate their study individually and as a group is lacking. Nowadays, the study of chaperone genes benefits from the availability of genome sequences and a new protocol, chaperonomics, which we applied to elucidate the human <it>hsp70 </it>family.</p> <p>Results</p> <p>We identified 47 hsp70 sequences, 17 genes and 30 pseudogenes. The genes distributed into seven evolutionarily distinct groups with distinguishable subgroups according to phylogenetic and other data, such as exon-intron and protein features. The N-terminal ATP-binding domain (ABD) was conserved at least partially in the majority of the proteins but the C-terminal substrate-binding domain (SBD) was not. Nine proteins were typical Hsp70s (65–80 kDa) with ABD and SBD, two were lighter lacking partly or totally the SBD, and six were heavier (>80 kDa) with divergent C-terminal domains. We also analyzed exon-intron features, transcriptional variants and protein structure and isoforms, and modality and patterns of expression in various tissues and developmental stages. Evolutionary analyses, including human <it>hsp70 </it>genes and pseudogenes, and other eukaryotic <it>hsp70 </it>genes, showed that six human genes encoding cytosolic Hsp70s and 27 pseudogenes originated from retro-transposition of HSPA8, a gene highly expressed in most tissues and developmental stages.</p> <p>Conclusion</p> <p>The human <it>hsp70</it>-gene family is characterized by a remarkable evolutionary diversity that mainly resulted from multiple duplications and retrotranspositions of a highly expressed gene, HSPA8. Human Hsp70 proteins are clustered into seven evolutionary Groups, with divergent C-terminal domains likely defining their distinctive functions. These functions may also be further defined by the observed differences in the N-terminal domain.</p

Evolution of dietary diversity and a starvation driven cross-diffusion system as its singular limit

We rigorously prove the passage from a Lotka-Volterra reaction-diffusion system towards a cross-diffusion system at the fast reaction limit. The system models a competition of two species, where one species has a more diverse diet than the other. The resulting limit gives a cross-diffusion system of a starvation driven type. We investigate the linear stability of homogeneous equilibria of those systems and rule out the possibility of Turing instability. Numerical simulations are included which are compatible with the theoretical results.Comment: Journal of Mathematical Biology, Springer Verlag (Germany), 202

Artigianati, manifatture e protoindustrie fra città e campagna: la Lombardia del XVI secolo

Al centro di questo contributo sta il tema della protoindustrializzazione e la discussione di tale modello interpretativo a partire dalla sua declinazione nel caso lombardo

Artigianati, manifatture e protoindustrie fra città e campagna: la Lombardia del XVI secolo

Al centro di questo contributo sta il tema della protoindustrializzazione e la discussione di tale modello interpretativo a partire dalla sua declinazione nel caso lombardo

Storia della filosofia medievale e laicità

I medievisti ovviamente più degli antichisti - osserva G. Duby - sono strana gente simile agli antropologi, persone che evadono dal loro presente partendo per l'XI secolo invece che per Samoa o per le isole Trobriand e fuggono dal loro mondo per sprofondare nelle radici

Chaperonin genes on the rise: new divergent classes and intense duplication in human and other vertebrate genomes

<p>Abstract</p> <p>Background</p> <p>Chaperonin proteins are well known for the critical role they play in protein folding and in disease. However, the recent identification of three diverged chaperonin paralogs associated with the human Bardet-Biedl and McKusick-Kaufman Syndromes (BBS and MKKS, respectively) indicates that the eukaryotic chaperonin-gene family is larger and more differentiated than previously thought. The availability of complete genome sequences makes possible a definitive characterization of the complete set of chaperonin sequences in human and other species.</p> <p>Results</p> <p>We identified fifty-four chaperonin-like sequences in the human genome and similar numbers in the genomes of the model organisms mouse and rat. In mammal genomes we identified, besides the well-known CCT chaperonin genes and the three genes associated with the MKKS and BBS pathological conditions, a newly-defined class of chaperonin genes named CCT8L, represented in human by the two sequences CCT8L1 and CCT8L2. Comparative analyses from several vertebrate genomes established the monophyletic origin of chaperonin-like MKKS and BBS genes from the CCT8 lineage. The CCT8L gene originated from a later duplication also in the CCT8 lineage at the onset of mammal evolution and duplicated in primate genomes. The functionality of CCT8L genes in different species was confirmed by evolutionary analyses and in human by expression data. Detailed sequence analysis and structural predictions of MKKS, BBS and CCT8L proteins strongly suggested that they conserve a typical chaperonin-like core structure but that they are unlikely to form a CCT-like oligomeric complex. The characterization of many newly-discovered chaperonin pseudogenes uncovered the intense duplication activity of eukaryotic chaperonin genes.</p> <p>Conclusions</p> <p>In vertebrates, chaperonin genes, driven by intense duplication processes, have diversified into multiple classes and functionalities that extend beyond their well-known protein-folding role as part of the typical oligomeric chaperonin complex, emphasizing previous observations on the involvement of individual CCT monomers in microtubule elongation. The functional characterization of newly identified chaperonin genes will be a challenge for future experimental analyses.</p

Dynamics of allosteric transitions in GroEL

The chaperonin GroEL-GroES, a machine which helps some proteins to fold, cycles through a number of allosteric states, the $T$ state, with high affinity for substrate proteins (SPs), the ATP-bound $R$ state, and the $R^{\prime\prime}$ ($GroEL-ADP-GroES$) complex. Structures are known for each of these states. Here, we use a self-organized polymer (SOP) model for the GroEL allosteric states and a general structure-based technique to simulate the dynamics of allosteric transitions in two subunits of GroEL and the heptamer. The $T \to R$ transition, in which the apical domains undergo counter-clockwise motion, is mediated by a multiple salt-bridge switch mechanism, in which a series of salt-bridges break and form. The initial event in the $R \to R^{\prime\prime}$ transition, during which GroEL rotates clockwise, involves a spectacular outside-in movement of helices K and L that results in K80-D359 salt-bridge formation. In both the transitions there is considerable heterogeneity in the transition pathways. The transition state ensembles (TSEs) connecting the $T$, $R$, and $R^{\prime\prime}$ states are broad with the the TSE for the $T \to R$ transition being more plastic than the $R\to R^{\prime\prime}$ TSE. The results suggest that GroEL functions as a force-transmitting device in which forces of about (5-30) pN may act on the SP during the reaction cycle.Comment: 32 pages, 10 figures (Longer version than the one published