A method to recognize distant repeats in protein sequences

An automated algorithm is presented that delineates protein sequence fragments which display similarity. The method incorporates a selection of a number of local nonoverlapping sequence alignments with the highest similarity scores and a graphtheoretical approach to elucidate the consistent start and end points of the fragments comprising one or more ensembles of related subsequences. The procedure allows the simultaneous identification of different types of repeats within one sequence. A multiple alignment of the resulting fragments is performed and a consensus sequence derived from the ensemble(s). Finally, a profile is constructed form the multiple alignment to detect possible and more distant members within the sequence. The method tolerates mutations in the repeats as well as insertions and deletions. The sequence spans between the various repeats or repeat clusters may be of different lengths. The technique has been applied to a number of proteins where the repeating fragments have been derived from information additional to the protein sequences. © 1993 Wiley-Liss, Inc.     

Hereditary variation of ciliary patterns in ciliated protozoa

Summary— In ciliates, the basic pattern of ciliature consists of longitudinal polarized ciliary rows. This basic pattern is expected to be retained through successive binary fissions by means of the so-called cytotactic mechanisms, as a consequence of autogenetic proliferation of basal bodies within each row. This idea is supported by the hereditary transmission of 180° rotated rows in Tetrahymena and Paramecium. These mechanisms should theoretically ensure intraclonal homogeneity for ciliary row number. In fact, some alterations are responsible for either loss or addition of rows. Such alterations are not strictly random processes, since they have been shown to be controlled by nuclear genes. Cytotaxis does not account for exact positioning of primordia for complex structures (buccal ciliature, for instance): the sites of basal body proliferation are determined by certain “positional information” which, in turn, is controlled by chromosomal genetic material more or less independently of pre-existing structures, as illustrated by many spontaneous or induced mutations. All deviations from the wild-type phenotype seem to be associated with very reduced fitness, at least in laboratory conditions. On the other hand, the currently known variants cannot account for intraspecific diversity. Thus, the evolutionary significance of these phenomena remains somewhat obscure.     

Dynamics of ruminal ciliated protozoa in feedlot cattle.

Fluctuations in ciliated protozoan concentrations were monitored in 40 individually fed crossbred heifers that were stepped up to an 85% concentrate diet either slowly (12 days) or rapidly (3 days), with or without monensin (30 ppm). Ruminal fluid was withdrawn from all animals by stomach tube at the start of the study, after each group reached full feed, and at 14-day intervals thereafter throughout the finishing period until termination (day 119). Neither monensin nor speed of step-up affected (P greater than 0.10) total protozoan concentrations, ruminal pH, or lactic acid concentrations. Average protozoan concentrations peaked on day 5, progressively declined until day 56, and then increased (P less than 0.05), suggesting an adaptation to ruminal conditions. Concentrations of Isotricha spp. were higher (P less than 0.05) on the final two sampling dates than at any other time. After day 28, Entodinium, Isotricha, and Polyplastron were the only surviving genera. Protozoa were not detected in 11 heifers on day 42 and day 56, but only two animals were defaunated on day 119, indicating either exogenous or endogenous refaunation. Average protozoan concentrations were not different (P greater than 0.25) between ruminal samples collected by stomach tube the day before slaughter (2.8 x 10(5)/g) and digesta samples collected the next day (1.6 x 10(5)/g). In feedlot cattle, defaunation apparently is transitory and individual animals harbor a dynamic protozoan population that fluctuates in response to changing ruminal conditions.     

The interstitial ciliated protozoa of a Mediterranean microcommunity

The main features of an interstitial ciliate community, living in the coastal sand of the Mediterranean sea, were analyzed during a one-year survey, carried out on 113 samples. The community was composed of 56 species, 31 of which belong to 8 resident genera. Total density varied from 0 to 410 individuals cm^–3 and followed a Spring-Summer and an Autumn-Winter trend, not related to temperature or to any single abiotic variable (interstitial dissolved O₂, grain sand size, salinity), although the density of some taxa was related to one abiotic factor. During Spring, diversity increased by a synchronous bloom involving the whole community. Some taxa, such as the predator Lacrymaria and its prey Frontonia, were significantly associated. The finding of the simultaneous bloom of congeneric species, like that of the genus Remanella suggests that they respond to the same environmental factors, and avoid interspecific competition.     

RCC1-like repeat proteins: a pangenomic, structurally diverse new superfamily of beta-propeller domains

The beta-propeller fold is a phylogenetically widespread, common protein architecture able to support a range of different functions such as catalysis, ligand binding and transport, regulation and protein binding. Interestingly, it appears that the beta-propeller topology is also compatible with strikingly diverse sequences. Amongst this diversity, there are three large groups of proteins with related sequences and very important cellular and intercellular regulatory functions: WD, kelch, and YWTD proteins. A common characteristic between these protein families is that their sequences, while distinct, all contain internal repeats 40-45 residues long. Through a pangenomic analysis using internal repeat profiles derived from the structurally known propeller modules of the eukaryotic protein RCC1 and the related prokaryotic protein BLIP-II, we have defined a new superfamily of propeller repeats, the RCC1-like repeats (RLRs). These sequences turn out to be more phylogenetically widespread than other large groups of propeller proteins, occurring in both prokaryotic and eukaryotic genomes. Interestingly, our research showed that RLR domains with different numbers of repeats exist, ranging from 3 to 7, and possibly more. A novel, intriguing finding is the discovery of sequences with 3 repeats, as well as proteins with 10 modular units, though in the latter case it is not clear whether these are made of two 5-bladed domains or a single, novel 10-bladed propeller. In addition, the results indicate that circular permutation events may have taken place in the evolution of these proteins. It is now established that the group of RLR proteins is extremely numerous and is characterized by unique, remarkable features which place it in a position of special interest as an important superfamily of proteins in nature.     

A comparative study of ciliated protozoa communities in activated-sludge plants

Abstract: Ciliated protozoa present in ten activated sludge plants at Madrid (Spain) were identified. The abundance of key groups of ciliates was determined at each plant; attached ciliates made up the most abundant and representative group. Multivariate statistical analysis was employed to study relationships between ciliates and both the physico-chemical and operational parameters of the plants. Partial correlation analysis revealed: (1) The indicator value of attached ciliates in assessing management and performance of the activated sludge process, (2) the relationship of swimming ciliates with short-aged sludges and lower quality effluents and (3) the direct association between swimming-crawling ciliates and bad settlement conditions of the sludge. Factor analysis showed the associations of the most frequent species of ciliates with the operational parameters of the plants, suggesting the indicator value of some of the species: Vorticella striata was related with poor quality of effluent; Aspidisca cicada with stable plant conditions, and Litonotus lamella with a deficiently settling sludge.     

Evolutionary analysis of amino acid repeats across the genomes of 12 Drosophila species

Repeated motifs of amino acids within proteins are an abundant feature of eukaryotic sequences and may catalyze the rapid production of genetic and even phenotypic variation among organisms. The completion of the genome sequencing projects of 12 distinct Drosophila species provides a unique dataset to study these intriguing sequence features on a phylogeny with a variety of timescales. We show that there is a higher percentage of proteins containing repeats within the Drosophila genus than most other eukaryotes, including non-Drosphila insects, which makes this collection of species particularly useful for the study of protein repeats. We also find that proteins containing repeats are overrepresented in functional categories involving developmental processes, signaling, and gene regulation. Using the set of 1-to-1 ortholog alignments for the 12 Drosophila species, we test the ability of repeats to act as reliable phylogenetic signals and find that they resolve the generally accepted phylogeny despite the noise caused by their accelerated rate of evolution. We also determine that in general the position of repeats within a protein sequence is non-random, with repeats more often being absent from the middle regions of sequences. Finally we find evidence to suggest that the presence of repeats is associated with an increase in evolutionary rate upon the entire sequence in which they are embedded. With additional evidence to suggest a corresponding elevation in positive selection we propose that some repeats may be inducing compensatory substitutions in their surrounding sequence.     

Chromosome-specific distribution of nucleotide substitutions in telomeric repeats of rice (Oryza sativa L.)

Examination of the genomic sequence of the telomere region makes it possible to understand the evolution of the structure of chromosomal ends. We compared the genomic sequences of 14 chromosomal ends of rice, Oryza sativa, L., on the basis of the variation in TTTAGGG repeats. In the proximal telomere repeats, nucleotide substitution occurred more frequently than in the more distal repeats. The most significant diversity was observed at the 1st, 2nd, or 3rd position of TTTAGGG, suggesting that T has been a target of mutation preferentially. Copies of ATTAGGG, CTTAGGG, GTTAGGG, TTCAGGG, TTGAGGG, or TATAGGG were arrayed in tandem, or the same subtypes were located close to each other. The substituted variants were accumulated in chromosomes 2L, 3L, 7L, and 10S but not in the ends of the other chromosomes. In contrast, deletion variants, almost all of which were TTTAGGG to TTAGGG, were dispersed over approximately 4.9% of the sequenced telomere repeats. In summary, the rice proximal telomeric arrays were composed of blocks of at least 6 types of substituted variants and the canonical sequence in a chromosome-specific manner. These results suggest that the variants might arise from the rapid expansion of a single mutation rather than from the gradual accumulation of random mutations.     

Conserved motifs and dynamic aspects of the terminal inverted repeat organization within <Emphasis Type="Italic">Bari</Emphasis>-like transposons

In this work the structural variations of Terminal Inverted Repeats (TIR) of Bari like transposons in Drosophila species has been studied. The aim is to try and assess the relevance of different variants in the evolutionary distribution of Bari elements. Bari is a member of the widespread Tc1 superfamily of transposable elements that has colonized most species of the Drosophila genus. We previously reported the structure of two related elements that differ in their TIR organization: Bari1 harbouring 26-bp TIR (short TIRs) and Bari2 with about 250-bp TIR (long TIR). While elements with short TIRs are complete and potentially autonomous, long ones are invariably composed of defective copies. The results show that in D. pseudobscura, D. persimilis and D. mojavensis, there is a third class of Bari elements, Bari3, that exhibit a long TIR structure and are not defective. Phylogenetic relationships among reconstructed transposases are consistent with the three subfamilies sharing a common origin. However, the final TIR organization into long or short structure is not related by descent but appears to be lineage-specific. Furthermore, we show that, independently of origin and organization, within the 250-bp terminal sequences there are three regions that are conserved in both sequence and position suggesting they are under functional constraint. Nucleotide sequence data from this article have been deposited in the EMBL/GenBank databases with the accession numbers: AM493769, AM493770, AM493771, AM493772.     

Vertical and temporal heterogeneity of planktonic ciliated protozoa in a humic lake

Seasonal population dynamics and the vertical distribution ofciliates were studied in relation to the particular food resourcesoccurring in a humic and moderately acidic lake (Lake Vassivière).The abundance (1.4 x 10³–20.4 x 10³ cells l^–1 mean= 4.8 x 10³ cells l^–1) and biomass (0.5–34.6 µgC l^–1, mean = 6.0 µg C l^–1) of ciliated protozoawere low and close to values reported for oligotrophic environments.The species composition of the population varied greatly withdepth. Whereas large-sized species of oligotrichs, some of whichwere mixotrophic, dominated at the surface, haptorids were bestrepresented in deep waters. The spatial distribution of thevarious groups of ciliates was largely determined by light andthe vertical distribution of microbial food resources (detritus,bacteria, algae) within the water column of this brown-coloredlake.     

Predation rates of flagellate and ciliated protozoa on bacterioplankton in a river

Abstract Predation rates of flagellate and ciliate protozoa on the bacterioplankton of Butrón River (Spain) were determined from FLB (fluorescently labelled bacteria) uptake rates. Bacterial and ciliate protozoa counts were higher when higher water temperature was recorded. Flagellate counts did not show this pattern, which suggested predation of flagellates by other organisms, or some other different nutritional mode besides phagotrophy. Average individual ciliate predation rates were up to 40-times higher than those of flagellates. These results were compared with similar data obtained from other authors in several aquatic systems. However, the population predation rates of flagellate protozoa were on average 6-times higher than that of ciliate protozoa, due to the low population numbers of the latter. Thus, flagellate protozoa can be considered as more important bacterial consumers than ciliates in this aquatic system.     

不同染色方法揭示纤毛原生动物草履虫接合生殖过程的新细节

通过石炭酸品红、Hoechst 33342、蛋白银及免疫荧光标记等染色方法对草履虫接合生殖过程进行了重新观察,结果发现:1)新月核是第一次减数分裂前期小核的主要形态学特征,在核内有一未被石炭酸品红、Hoechst 33342着色区域,蛋白银染色则清楚显示该结构;2)4个单倍体减数分裂产物中的1个核进入口旁锥完成配前第三次核分裂,其余3核退化.蛋白银染色和抗α微管蛋白单克隆抗体进行免疫荧光标记显示,核进入口旁锥的时期在第二次减数分裂末期而非减数分裂结束后;3)配前第三次分裂末期,核间连丝的中间段有一被蛋白银识别的结构,但免疫荧光标记却无显示,只表现为纤维状结构与两侧核间连丝相连.观察结果为草履虫接合生殖过程中相关分子生物学机制研究奠定了必要的形态学基础.     

Moderation of ruminal fermentation by ciliated protozoa in cattle fed a high-grain diet.

The objective of this study was to assess the influence of ciliated protozoa on ruminal fermentation in cattle fed high-grain diets. Six ruminally cannulated steers fed a corn-based grain diet (85% concentrate plus 15% alfalfa hay) at 12-h intervals were assigned randomly to two groups, ciliate free and faunated, in a crossover design. Defaunation was by ruminal emptying, omasal flushing, and treatment with sodium sulfosuccinate. Two to 3 weeks after defaunation, the ruminal contents of all steers were sampled before the morning feeding (0 h) and at 1, 2, 4, 6, 8, and 12 h after feeding to measure pH, analyze fermentation products, and monitor counts of ciliated protozoa and lactic acid-producing and -fermenting bacterial groups. Total numbers of ciliated protozoa in the faunated steers averaged 4.3 x 10(5)/g, and the protozoa consisted of nine genera. Ciliate-free steers had lower (P less than 0.01) ruminal pHs (pH 5.97) than faunated cattle (pH 6.45); however, the treatment-time interaction was not significant. Ruminal lactate and ammonia concentrations were similar in both groups. The total volatile fatty acid concentration was higher (P less than 0.05) in the ciliate-free steers than in the faunated steers and exhibited a treatment-time interaction (P less than 0.05). The acetate-to-propionate ratio was higher (P less than 0.05) in the faunated group than in the ciliate-free group and showed a treatment-time interaction (P less than 0.05). Total anaerobic bacterial counts were about fourfold higher in the ciliate-free group than in the faunated group.(ABSTRACT TRUNCATED AT 250 WORDS)     

棘孢木霉丝裂原活化蛋白激酶基因task1的克隆及序列分析

为深入研究丝裂原活化蛋白激酶(Mitogen-activated protein kinase,MAPK)的功能,从棘孢木霉(Tricho-derma asperellum)中克隆了丝裂原活化蛋白激酶(MAPK)基因task1,并对其序列进行分析。该基因编码355个氨基酸,全长1 757 bp,理论分子质量41.1 kD,理论等电点为6.64,与深绿木霉(T.atroviride)MAPK基因tmk1、里氏木霉(T.reesei)MAPK基因tmkA和绿色木霉(T.virens)MAPK基因tmkA在氨基酸和核苷酸水平上同源性都很高,蛋白结构预测为丝氨酸/苏氨酸蛋白激酶。