Models of the Collective Behavior of Proteins in Cells: Tubulin, Actin and Motor Proteins

One of the most important issues of molecular biophysics is the complex and multifunctional behavior of the cell's cytoskeleton. Interiors of living cells are structurally organized by the cytoskeleton networks of filamentous protein polymers: microtubules, actin and intermediate filaments with motor proteins providing force and directionality needed for transport processes. Microtubules (MT's) take active part in material transport within the cell, constitute the most rigid elements of the cell and hence found many uses in cell motility (e.g. flagella andcilia). At present there is, however, no quantitatively predictable explanation of how these important phenomena are orchestrated at a molecular level. Moreover, microtubules have been demonstrated to self-organize leading to pattern formation. We discuss here several models which attempt to shed light on the assembly of microtubules and their interactions with motor proteins. Subsequently, an overview of actin filaments and their properties isgiven with particular emphasis on actin assembly processes. The lengths of actin filaments have been reported that were formed by spontaneous polymerization of highly purified actin monomers after labeling with rhodamine-phalloidin. The length distributions are exponential with a mean of about 7 μm. This length is independent of the initial concentration of actin monomer, an observation inconsistent with a simple nucleation-elongation mechanism. However, with the addition of physically reasonable rates of filament annealing and fragmenting, a nucleation-elongation mechanism can reproduce the observed average length of filaments in two types of experiments: (1) filaments formed from a wide range of highly purified actin monomer concentrations, and (2) filaments formed from 24 mM actin over a range of CapZ concentrations. In the final part of the paper we briefly review the stochastic models used to describe the motion of motor proteins on protein filaments. The vast majority of these models are based on ratchet potentials with the presence of thermal noise and forcing due to ATP binding and a subsequent hydrolysis. Many outstanding questions remain to be quantitatively addressed on a molecular level in order to explain the structure-to-function relationship for the key elements of the cytoskeleton discussed in this review. This revised version was published online in July 2006 with corrections to the Cover Date.     

Genetic Evidence for Functional Interactions between Actin Noncomplementing (Anc) Gene Products and Actin Cytoskeletal Proteins in Saccharomyces Cerevisiae

We describe here genetic interactions between mutant alleles of Actin-NonComplementing (ANC) genes and actin (ACT1) or actin-binding protein (SAC6, ABP1, TPM1) genes. The anc mutations were found to exhibit allele-specific noncomplementing interactions with different act1 mutations. In addition, mutant alleles of four ANC genes (ANC1, ANC2, ANC3 and ANC4) were tested for interactions with null alleles of actin-binding protein genes. An anc1 mutant allele failed to complement null alleles of the SAC6 and TPM1 genes that encode yeast fimbrin and tropomyosin, respectively. Also, synthetic lethality between anc3 and sac6 mutations, and between anc4 and tpm1 mutations was observed. Taken together, the above results strongly suggest that the ANC gene products contribute to diverse aspects of actin function. Finally, we report the results of tests of two models previously proposed to explain extragenic noncomplementation.     

Phylogenetic systematics of the reptantian Decapoda (Crustacea, Malacostraca)

Although the biology of the reptantian Decapoda has been much studied, the last comprehensive review of reptantian systematics was published more than 80 years ago. We have used cladistic methods to reconstruct the phylogenetic system of the reptantian Decapoda. We can show that the Reptantia represent a monophyletic taxon. The classical groups, the 'Palinura', 'Astacura' and 'Anomura' are paraphyletic assemblages. The Polychelida is the sister-group of all other reptantians. The Astacida is not closely related to the Homarida, but is part of a large monophyletic taxon which also includes the Thalassinida, Anomala and Brachyura. The Anomala and Brachyura are sister-groups and the Thalassinida is the sister-group of both of them. Based on our reconstruction of the sister-group relationships within the Reptantia, we discuss alternative hypotheses of reptantian interrelationships, the systematic position of the Reptantia within the decapods, and draw some conclusions concerning the habits and appearance of the reptantian stem species.     

Evolution of the thaumastocheliform lobsters (Crustacea,Decapoda, Nephropidae)

Deep‐sea lobsters previously assigned to the family Thaumastochelidae Bate, 1888, the thaumastocheliforms, have very distinctive, greatly unequal first chelipeds, with the right side extremely elongate and pectinate, and in having short, quadrate pleonal pleura. Despite interesting morphology and a long taxonomic history, the phylogeny of the group has received little detailed analysis. Here, we conduct a species‐level phylogenetic analysis of the thaumastocheliforms based on morphological and molecular data (three mitochondrial genes: COI, 16S rDNA and 12S rDNA; two nuclear protein‐coding genes: H3 and NaK) to robustly reconstruct their evolutionary history and estimate divergence times. Separate and combined analyses of all data sources support thaumastocheliform monophyly, but as a clade deeply nested within the Nephropidae supporting recent synonymy of Thaumastochelidae with Nephropidae. Combined and molecular‐only analyses support generic monophyly of all three thaumastocheliform genera and Dinochelus as sister to Thaumastochelopsis, fully corroborating the current, morphology‐based taxonomy. In contrast, Thaumastocheles is recovered as paraphyletic in morphology‐only analyses owing to minimal character support. The Cretaceous–Paleogene Oncopareia was recovered as a stem‐lineage thaumastocheliform. The fossil record indicates that the thaumastocheliforms once lived in shallow, continental shelf depths, but moved into deeper water in the Cenozoic where they occur today. The thaumastocheliforms originated in northern Europe during the Mid‐Late Cretaceous and later dispersed westwards to the south‐eastern Pacific through the western Atlantic and eastwards to the western Pacific through the Indian Ocean. Thaumastochelopsis can be considered the most derived thaumastocheliform genus based on the degree of structural reduction relative to other thaumastocheliforms, its remote geographical occurrence (Australia) from the hypothesised place of origin (northern Europe) and its more recent estimated divergence than other genera (28 Mya for the MRCA of extant species of the genus).     

Diel and Seasonal Changes in the Structure of a Decapod (Crustacea: Decapoda) Community of Cymodocea nodosa from Southeastern Spain (West Mediterranean Sea)

The study of a decapod community in a Cymodocea nodosa meadow from Southeastern Spain (Western Mediterranean Sea) showed a stable structure, in which the families Hippolytidae, Processidae, Majidae and Portunidae were the most abundant and the species Hippolyte niezabitowskii dominated. The animal community was more numerous and diverse during the night, showing the existence of nychthemeral movements, which are essentially related to the trophic behaviour and shelter. In this way, many species increased their abundance as a result of an increasing activity and, also, of an influx of other species and specimens from adjacent sandy bottoms, such as Processa spp. (mainly P. modica) Sicyonia carinata, Liocarcinus spp. (mainly juveniles) and several species of hermit crabs, which were rare or absent during the day. All these changes produced modifications in the dominance curves and in the values of all ecological indices (richness, diversity and evenness). Monthly samples were grouped and ordered (MDS) by the factor “day–night”, which showed slight qualitative and quantitative differences (SIMPER, dissimilarity average of the factor day–night = 61.67). On the other hand, no global seasonal differences have been found (one way ANOSIM), but there was a significant level of similarity between winter and spring, while the summer samples were the most different. The differentiation of the summer 1999 can be attributed to a decrease in species abundance and richness, probably due to the dynamics of the decapod populations and the balance with predators (fishes), while that of the summer 2000, to an anomalous event: the massive proliferation of filamentous algae, mainly Ectocarpus s.l., which modified the environmental conditions.     

Genetic Variation and Divergence in the Genus Carcinus (Crustacea,Decapoda)

The extent of genetic differentiation of the decapod crustaceans Carcinus maenas (L.) and C. aestuarii Nardo was studied in nine nearshore locations comprising various European marine and brackish-water habitats, (Norway, Germany, France, Spain, Italy and Yugoslavia), using starch gel electrophoresis. The heterozygosity for all 19 allozyme loci was 0.026–0.016 (C. maenas) and 0.011–0.003 (C. aestuarii); one locus (Pgm) was the most polymorphic. The populations had rather low levels of genetic variability, comparable to those found in other decapods. In general, a light clinal variation in allele frequencies was discovered at the Pgm locus of C. maenas as latitude decreased. Because of similar morphologies and a closed genetic relationship (I = 0.89), the two forms should be considered subspecies. Therefore, the designation of the Atlantic subspecies C. maenas maenas is proposed, and the term of the Mediterranean subspecies C. maenas aestuarii is recommended.     

An Ultrastructural Study of Spermatozoa of the Majidae with Particular Reference to the Aberrant Spermatozoon of Macropodia longirostris (Crustacea,Decapoda, Brachyura)

A total of 17 species, in 14 genera of majids have been examined for sperm ultrastructure. The present account describes the sperm of six of these species, in two subfamilies: Pisinae—Sphenocarcinus orbiculatus and Sphenocarcinus stuckiae and Inachinae—Cyrtomaia furici, Grypacheus hyalinus, Platymaia rebierei and Macropodia longirostris. M. longirostris has the only eubrachyuran sperm in which the acrosome is known to depart radically from a subspheroidal form. The acrosome is semilunar in shape and is bordered by a very thin layer of cytoplasm and an unusually uniform, narrow band of chromatin. The apical surface of the acrosome is almost flat, though slightly concave, whereas the posterior surface forms a hemisphere, and is almost completely occupied by the thin, centrally perforate, electron dense operculum. The bulk of the acrosome consists of a homogeneous, moderately electron dense outer acrosome zone. This surrounds a small inner acrosome zone internal to which is an ellipsoidal, pale perforatorium capped by a central acrosome zone. Majid sperm are distinguished by a flattened and/or centrally depressed operculum; a further characteristic is that the pointed perforatorium is relatively short and frequently does not reach the operculum. They vary inter alia with regard to presence or absence of a posterior median process and, apparently, of centrioles and of microtubules in the nuclear arms, and in the number of these arms. Perforation of the operculum, seen in the Pisinae, is not constant in the Inachinae. Spermatozoal ultrastructure offers no certain support for a close relationship of majids with parthenopids or hymenosomatids.     

The complete mitochondrial genome of the American lobster, Homarus americanus (Crustacea, Decapoda)

Although relatively a large number of the complete mitochondrial genome sequences have been determined from various decapod species (29 mtDNA sequences reported so far), the information for the infraorder Astacidea (including lobsters, crayfishes, and their relatives) is very limited and represented by only one complete sequence from the Australian freshwater crayfish species Cherax destructor. In this study, we determined the complete mitochondrial DNA sequence of Homarus americanus, the first representative of the family Nephropidae to be fully characterized. Comparison of the gene arrangement reveals that H. americanus mtDNA is identical to those of other pancrustacean species but differs from the other astacidean species (C. destructor). Based on these data, it can be assumed that an idiosyncratic gene order discovered in C. destructor mtDNA may be secondarily acquired from the ancestral lineage of the Astacidea.     

Zur Deutung der Carapaxfurchen der Astacidea (Crustacea, Decapoda)

The carapace grooves of decapod Crustacea are hitherto considered as remnants of somit boundaries. This hypothesis is rejected for theoretical reasons and on the basis of morphological studies of recent crayfishes and lobsters. The grooves are recognized as mechanically induced secondary structures resulting from the attachment of different muscles to the carapace. The grooves can be used for the diagnosis of certain systematic groups, but are of little value for phylogenetic considerations.     

Ageing and longevity in the Decapoda (Crustacea): A review

Ageing and longevity is a neglected field of crustacean biology. Information on longevity is available for less than 2% of the extant species of the Decapoda. Maximum ages reliably determined range from 40 days to 72 years corresponding to a life span difference of a factor of 650. The shortest-lived decapods are planktonic dendrobranchiate shrimps, and particularly long-lived species with life spans of decades are found in the Astacidea. Most decapods seem to live for 1-10 years. High geographical latitude, the deep sea and freshwater caves promote longevity. The majority of the Decapoda is indeterminately growing and presumably characterized by negligible senescence. The adults of the determinately growing decapods like some brachyuran crabs suffer from mechanical senescence and are unable to regenerate lost appendages. The decapod crustaceans have developed many effective anti-ageing mechanisms including moulting, detoxification of free radicals, removal of cellular waste, renewal of tissues by life-long stem cell activity, regeneration of appendages, detoxification of environmental pollutants and isolation of pathogens and diseased tissue areas by melanisation and encapsulation. Age related diseases including cancer are virtually unknown. The present compilation of data on longevity and senescence in decapods is the first one that covers the whole spectrum of a higher invertebrate taxon. It is hoped to provide an interesting source of information for carcinologists and biogerontologists. Further improvement of knowledge on ageing and longevity in the Decapoda would be beneficial for crustacean aquaculture, fisheries and ecological modelling. Some decapods even have good potential to become models for general ageing research.     

Lysmata seticaudata (Decapoda,Crustacea) als Putzergarnele im Mittelmeer

Members of the shrimp speciesLysmata seticaudata were observed to clean a morrey eel in the western Mediterranean Sea (Baleares, Spain). In contrast to the cleaning symbiosis of tropical shrimps, severalLysmata species have only one host, thus representing a primitive type of cleaning behaviour.Lysmata seticaudata is not dependent upon cleaning for food and usually these shrimps are found without a host.     

Studie der Astacidae (Crustacea,Decapoda) II. Teil

Ohne Zusammenfassung     

The complete mitochondrial genome of the Japanese mud shrimp Upogebia major (Crustacea, Decapoda)

We determined a full-length sequence of mitochondrial (mt) genome from Upogebia major. This is the first complete mt genome report for infraorder Thalassinidea in Decapoda, Crustacea. Our result showed that U. major generally followed a typical pancrustacean gene order but some tRNA genes showed a very unique gene arrangement such as duplication or translocation. Since none of the complete mt genome sequences in the infraorder Thalassinidea are available yet, this report will provide additional information in relation to mt genome diversity and evolution of the decapods.     

Microsatellite loci from the pink shrimp Farfantenaeus notialis (Crustacea,Decapoda)

Farfantepenaeus notialis is an important resource for fisheries in Cuba. For this reason and for a sustainable exploitation it is important to study their population structure and genetic variability. We report and characterize microsatellites as genetic markers from this species. Fifteen microsatellite polymerase chain reaction (PCR) primers were designed and tested in some individuals from different populations. Seven pair of primers showed reliable amplification products and five were polymorphic. The allele number ranged from 4 to 33, and the observed and expected heterozygosities were relatively high with values between 0.63 and 0.74 and 0.56 and 0.81, respectively. Departures from Hardy–Weinberg equilibrium were observed for all loci.     

Cleavage and gastrulation of the dendrobranchiate shrimp Penaeus monodon (Crustacea,Malacostraca, Decapoda)

The cleavage pattern of the black tiger shrimp Penaeus monodon was analyzed from the first division until gastrulation. Observations were based on microscopy combined with the use of fluorescent dyes, histological techniques, and computer based three-dimensional reconstructions. Early cleavage is holoblastic and follows a stereotypic pattern, which largely corresponds to what is known from other dendrobranchiate decapods. However, for the first time in this group, we report the presence of an intracellular structure throughout early development. This intracellular body (icb) marks the lineage of one of the two enlarged and division-delayed mesendoderm cells that initiate gastrulation. The identity of the icb as a natural marker and putative determinant of the germ line and its implications on the establishment of the body axes are discussed. The icb as a landmark reveals that the same stereotypic cell division pattern can lead to different fates of individual cells. Hence, the results of this study permit an additional approach to study the relation between cell lineage pattern and the identity of cell lineages.     

Constant morphological patterns in the hemolymph vascular system of crayfish (Crustacea,Decapoda)

We present a study of the hemolymph vascular system of the marbled crayfish, Procambarus fallax f. virginalis, the only crayfish species known to be parthenogenetic. To identify potential evolutionary patterns, we compared data from a total of 48 specimens of P. fallax with 22 specimens of Orconectes limosus. Visualizations (2D and 3D) were carried out using a combination of classical and modern morphological techniques. Our data were compared to the existing literature.Like all Decapoda, both P. fallax and O. limosus have a hemolymph vascular system, consisting of a globular heart with seven off-branching arteries. We were able to visualize in detail the heart of crayfish for the first time, i.e., the myocard with its clusters of muscles running through the lumen of the heart, the valves and flaps of ostia and arteries. Furthermore, the branching patterns of the seven artery systems were analyzed. Anatomical structures identified to be consistent in all specimens of both species were combined as ground pattern of hemolymph vascular system features for Astacida.     

Seasonal variations in the intermediate metabolism of Parastacus varicosus (Crustacea, Decapoda, Parastacidae)

The aim of this study was to analyze the seasonal variations in the metabolism of Parastacus varicosus and examine the possible relationships to its reproduction. Animals were sampled (9 h to 10 h) in each month in the Gravataí River, RS, Brazil. Haemolymph samples were collected from each crayfish in the field for determination of glucose, total proteins, total lipids, and total cholesterol. Hepatopancreas, abdominal muscle, and gonads were removed for determination of glycogen, total proteins, total lipids, and total cholesterol. ANOVA revealed significant seasonal differences in the biochemical composition of all tissues studied; when the sexes were compared these parameters did not show any significant difference in the hepatopancreas and muscle. However, in haemolymph we observed significant variation only in cholesterol and lipid levels. The results suggest that the metabolic variability is related to the stage of maturation of the gonads, in females, where the hepatopancreas and other tissue studies can store and transfer reserves to support maturation to complement the food intake. Variations in the gonadosomatic and hepatosomatic indices suggest that reproduction occurs principally in summer. As in other decapods, abiotic factors such as water temperature, oxygen content, etc. influence the intermediate metabolism.