The cardinal principle of like attracting like generates many ubiquitous oligopeptides shared by divergent proteins

Phenotypic and genetic variation in the response of chickens to Eimeria tenella induced coccidiosis

BACKGROUND

Coccidiosis is a major contributor to losses in poultry production. With emerging constraints on the use of in-feed prophylactic anticoccidial drugs and the relatively high costs of effective vaccines, there are commercial incentives to breed chickens with greater resistance to this important production disease. To identify phenotypic biomarkers that are associated with the production impacts of coccidiosis, and to assess their covariance and heritability, 942 Cobb500 commercial broilers were subjected to a defined challenge with Eimeria tenella (Houghton). Three traits were measured: weight gain (WG) during the period of infection, caecal lesion score (CLS) post mortem, and the level of a serum biomarker of intestinal inflammation, i.e. circulating interleukin 10 (IL-10), measured at the height of the infection.

RESULTS

Phenotypic analysis of the challenged chicken cohort revealed a significant positive correlation between CLS and IL-10, with significant negative correlations of both these traits with WG. Eigenanalysis of phenotypic covariances between measured traits revealed three distinct eigenvectors. Trait weightings of the first eigenvector, (EV1, eigenvalue = 59%), were biologically interpreted as representing a response of birds that were susceptible to infection, with low WG, high CLS and high IL-10. Similarly, the second eigenvector represented infection resilience/resistance (EV2, 22%; high WG, low CLS and high IL-10), and the third eigenvector tolerance (EV3, 19%; high WG, high CLS and low IL-10), respectively. Genome-wide association studies (GWAS) identified two SNPs that were associated with WG at the suggestive level.

CONCLUSIONS

Eigenanalysis separated the phenotypic impact of a defined challenge with E. tenella on WG, caecal inflammation/pathology, and production of IL-10 into three major eigenvectors, indicating that the susceptibility-resistance axis is not a single continuous quantitative trait. The SNPs identified by the GWAS for body weight were located in close proximity to two genes that are involved in innate immunity (FAM96B and RRAD).

EXTENSIN18 is required for full male fertility as well as normal vegetative growth in Arabidopsis

EXTENSINS (EXTs) are a 65-member subfamily of hydroxyproline-rich glycoproteins (HRGPs) of which 20 putatively form crosslinking networks in the cell wall. These 20 classical EXTs are involved at the start of new wall assembly as evidenced by a requirement for EXT3 during cytokinesis, and the ability of some EXTs to polymerize in vitro into dendritic patterns. EXT3 was previously shown to form pulcherosine (three Tyrosines) cross-links. Little direct data exists on the other 19 classical EXTs. Here, we describe the phenotypes of ext18 mutants and rescued progeny as well as associated expression profiles of all 20 classical EXT genes. We found that EXT18 is required for full male fertility, as well as for normal vegetative growth. EXT18 has potential to form crosslinking networks via di-iso-di-tyrosine (four Tyrosines) covalent bonds, and not via pulcherosine due to deficit of lone Tyrosines. This together with ext18 defective pollen grains and pollen tubes, and reduced plant size, suggests that EXT18-type EXTs are important contributors to wall integrity, in pollen and other rapidly extending walls. The data also show that a knockout of EXT18 had a pleiotropic affect on the expression of several EXTs, as did the reintroduction of the native EXT18 gene, thus supporting the thesis that transcription of groups of EXTs are co-regulated and work in different combinations to make distinctive inputs into wall assembly of different cell types. These insights contribute to basic knowledge of cell wall self-assembly in different cell types, and potentially enable biotechnological advances in biomass increase and plant fertility control.

Self-assembly of the plant cell wall requires an extensin scaffold

Cytokinesis partitions the cell by a cleavage furrow in animals but by a new cross wall in plants. How this new wall assembles at the molecular level and connects with the mother cell wall remains unclear. A lethal Arabidopsis embryogenesis mutant designated root-, shoot-, hypocotyl-defective (rsh) provides some clues: RSH encodes extensin AtEXT3, a structural glycoprotein located in the nascent cross wall or "cell plate" and also in mature cell walls. Here we report that electron micrographs of rsh mutant cells lacking RSH extensin correspond to a wall phenotype typified by incomplete cross wall assembly. Biochemical characterization of the purified RSH glycoprotein isolated from wild-type Arabidopsis cell cultures confirmed its identity as AtEXT3: a (hydroxy)proline-rich glyco protein comprising 11 identical amphiphilic peptide repeats with a 28-residue periodicity: SOOOOKKHYVYKSOOOOVKHYSOOOVYH (O = Hyp), each repeat containing a hydrophobic isodityrosine cross-link motif (YVY, underlined). Atomic force microscopy of RSH glycoprotein imaged its propensity for self-assembly into a dendritic scaffold. Extensin peroxidase catalyzed in vitro formation of insoluble RSH gels with concomitant tyrosine cross-linking, hence this likelihood in muro. We conclude that self-assembling amphiphiles of lysine-rich RSH extensin form positively charged scaffolds in the cell plate. These react with negatively charged pectin to create an extensin pectate coacervate that may template further orderly deposition of the new cross wall at cytokinesis.

Differentiation of European cattle by AFLP fingerprinting

The Neolithic introduction of domestic cattle into Europe was followed by differential adaptation, selection, migration and genetic isolation, leading ultimately to the emergence of specialized breeds. We have studied the differentiation of European cattle by amplified fragment length polymorphism (AFLP) fingerprinting. Combining AFLP data sets from two laboratories yielded 81 biallelic polymorphic markers scored in 19-22 individual animals from 51 breeds. Model-based clustering differentiated Podolian cattle as well as French and Alpine breeds from other European cattle. AFLP genetic distances correlated well with microsatellite-based genetic distances calculated for the same breeds. However, the AFLP data emphasized the divergence of taurine and indicine cattle relative to the variation among European breeds and indicated an Eastern influence on Italian and Hungarian Podolian breeds. This probably reflects import from the East after the original introduction of domestic cattle into Europe. Our data suggest that Italian cattle breeds are relatively diverse at the DNA sequence level.

Close genetic relationship of early neolithic cattle from Ziegelberg (Freising, Germany) with modern breeds

In 2003 a variety of crafts and bone specimens were found during excavations of a Neolithic settlement near Freising, the southernmost site of the Linear Pottery Culture in Bavaria. Six cattle bones were used to extract ancient DNA (aDNA). Applying nested and touchdown PCR, two fragments of the mitochondrial (mt) DNA control region could be amplified from specimen 533/III which yielded a total of 230 base pairs (bp). The sequence was compared with the homologous part of 40 extant breeds of Bos taurus and B. indicus and related species, such as Banteng (B. javanicus), Gaur (B. gaurus), the European bison (Bison bonasus) and the aurochs (B. primigenius). A neighbour joining tree was constructed based on the appropriate model of sequence evolution. The control region sequence of the 533/III cattle bone, whose age was determined by radiocarbon dating, clusters close to the extant European breeds, but distinctly apart from the basal aurochs and far distant from the B. indicus group. The archaeological and genetic analyses of Bos Ziegelberg demonstrate that domesticated cattle reached southern Bavaria at least 7000 years ago.

Gum arabic glycoprotein contains glycomodules of both extensin and arabinogalactan-glycoproteins

Gum arabic glycoprotein (GAGP) is a large molecular weight, hydroxyproline-rich arabinogalactan-protein (AGP) component of gum arabic. GAGP has a simple, highly biased amino acid composition indicating a repetitive polypeptide backbone. Previous work (Qi, W., Fong, C., Lamport, D.T.A., 1991. Plant Physiology 96, 848), suggested small (approximately 11 residue) repetitive peptide motifs each with three Hyp-arabinoside attachment sites and a single Hyp-arabinogalactan polysaccharide attachment site. We tested that hypothesis by sequence analysis of the GAGP polypeptide after HF-deglycosylation. A family of closely related peptides confirmed the presence of a repetitive 19-residue consensus motif. However, the motif: Ser-Hyp-Hyp-Hyp-Thr-Leu-Ser-Hyp-Ser- Hyp-Thr-Hyp-Thr-Hyp-Hyp-Leu-Gly-Pro-His, was about twice the size anticipated. Thus, judging by Hyp-glycoside profiles of GAGP, the consensus motif contained six Hyp-arabinosides rather than three and two Hyp-polysaccharides rather than one. We inferred the glycosylation sites based on the Hyp contiguity hypothesis which predicts arabinosides on contiguous Hyp residues and arabinogalactan polysaccharides on clustered non-contiguous Hyp residues, i.e. the GAGP motif would consist of arabinosylated contiguous Hyp blocks flanking two central Hyp-polysaccharides. We predict this rigidifies the glycoprotein, enhances the overall symmetry of the glycopeptide motif, and may explain some of the remarkable properties of gum arabic.

Geographic distribution and frequency of a taurine Bos taurus and an indicine Bos indicus Y specific allele amongst sub-saharan African cattle breeds

We report for the first time, and for the whole of sub-Saharan Africa, the geographical distribution and the frequency of an indicine and a taurine Y specific allele amongst African cattle breeds. A total of 984 males from 69 indigenous African populations from 22 countries were analysed at the microsatellite locus INRA 124. The taurine allele is probably the oldest one on the continent. However, the taurine and the indicine alleles were present in 291 males (30%), and 693 males (70%), respectively. More particularly, 96% of zebu males (n = 470), 50% of taurine males (n = 263), 29% of sanga males (crossbreed Bos taurus x Bos indicus, n = 263) and 95% of zebu x sanga crossbred males (n = 56) had the indicine allele. The Borgou, a breed classified as zebu x taurine cross showed only the zebu allele (n = 12). The indicine allele dominates today in the Abyssinian region, a large part of the Lake Victoria region and the sahelian belt of West Africa. All the sanga males (n = 64) but only one from the Abyssinian region had the indicine allele. The taurine allele is the commonest only among the sanga breeds of the southern African region and the trypanotolerant taurine breeds of West Africa. In West Africa and in the southern Africa regions, zones of introgression were detected with breeds showing both Y chromosome alleles. Our data also reveal a pattern of male zebu introgression in Mozambique and Zimbabwe, probably originating from the Mozambique coast. The sanga cattle from the Lake Victoria region and the Kuri cattle of Lake Chad, cattle populations surrounded by zebu breeds were, surprisingly, completely devoid of the indicine allele. Human migration, phenotypic preferences by the pastoralists, adaptation to specific habitats and to specific diseases are the main factors explaining the present-day distribution of the alleles in sub-Saharan Africa.

Correlations and anticorrelations among nucleotide distributions along the genomes of various organisms

We have analyzed correlations of nucleotide distributions along more than 50 megabases of the longest sequenced parts of the human, mouse, Drosophila, Arabidopsis, yeast, E.coli and three kinds of viral genomes. The strongest correlations were observed between the distributions of C and G, in particular in the genome of Drosophila. This correlation was much weaker, though still strong, in the human genome and E.coli that exhibited the same level of this correlation. The C/G correlation hardly originates from the isochores because the isochores were not reported to occur in the genomes of Drosophila and E. coil. The genomic distribution curves of adenine and thymine were also positively correlated in all analyzed organisms except for the yeast where they were anticorrelated. Still stronger anticorrelations were, however, observed between the genomic distributions of A and C and between G and T. These genomic distributions anticorrelated almost generally and very strong. These anticorrelations are likely to originate from point mutations resulting from unrepaired GA mispairing as a replication intermediate. The C/A or G/T anticorrelation or compensation is a very strong and general new phenomenon that shapes the genomic nucleotide sequences.

Susceptibility of the Namchi and Kapsiki cattle of Cameroon to trypanosome infection

Two indigenous Cameroonian taurine cattle breeds (Namchi and Kapsiki) were evaluated for trypanosusceptibility following inoculation with Trypanosoma congolense. The degree of zebu ancestry in the experimental animals was assessed using 6 microsatellite markers which are known to have certain unique alleles which are diagnostic of Bos indicus genetic input. Their response to the infection was compared to that of known trypanotolerant (N'Dama) and trypanosusceptible (Ngaoundere Gudali) cattle. The Namchi and the N'Dama controlled the development and severity of anaemia and parasitaemia better than the Kapsiki and the Gudali. For these parameters, there was no significant difference between the N'Dama and Namachi nor between the Kapsiki and Gudali. Similarly, weight loss showed significant breed variation. The N'Dama lost the least weight and the Kapsiki the most. Zebu introgression in the Namchi was comparable to that in the N'Dama while that of the Kapsiki breed was higher, indicating a high level of cross breeding. From the results, the Namchi are considered trypanotolerant while the Kapsiki are trypanosusceptible. The potential exploitation of the indigenous Namchi cattle is discussed.

Nucleotide diversity of mitochondrial DNAs between the swamp and the river types of domestic water buffaloes, Bubalus bubalis, based on restriction endonuclease cleavage patterns

Cleavage patterns of mitochondrial DNAs (mtDNAs) by 15 restriction endonucleases were analyzed for 10 swamp and 13 river types of domestic water buffaloes. Digestions with nine enzymes exhibited polymorphisms giving two or three kinds of cleavage patterns. Five mtDNA types were identified, three types in the swamp buffaloes of the Philippines, Vietnam, and Indonesia (S-types) and two types in the river buffaloes of Bangladesh and Pakistan (R-types). Nucleotide diversities ranged from 0.2 to 0.6% within the S- and R-types and from 1.9 to 2.4% between the R-types and the S-types. These values indicated that R-type and S-type mtDNAs differentiated at the subspecific level of other mammalian species reported. The possibility of polyphyletic domestication in different places is discussed for the origin of two distinct types of domestic water buffaloes.

Diverse incidences of individual oligopeptides (dipeptidic to hexapeptidic) in proteins of human, bakers' yeast, and Escherichia coli origin registered in the Swiss-Prot data base

Oligopeptidic permutations of the 20 amino acid residues give rise to proteins of diverse functions. Our long-term goal is to produce a lexicon of oligopeptides, classifying them into at least five categories: (i) ubiquitous, (ii) function specific, (iii) group specific, (iv) species specific, and (v) nonexistent. To begin with, we report on the varying frequencies of individual oligopeptides (dipeptidic to hexapeptidic in length) found among 2862 human proteins, 1942 Saccharomyces cerevisiae proteins, and 2672 Escherichia coli proteins registered in the Swiss-Prot data base (version 29.0, released in June 1994). At all lengths (dipeptides to hexapeptides), homooligopeptides were very prominent among the most frequently occurring varieties in proteins of human and bakers' yeast origins. However, this was not the case with E. coli. While all of the expected 20(3) varieties of tripeptides were found among human proteins, three tripeptides (Cys-Cys-Trp, Trp-Trp-Cys, and Trp-Trp-His) were missing from the bakers' yeast proteins. Three tripeptides (Cys-Ile-Trp, Cys-Met-Tyr, and Cys-Trp-Trp) were also absent from E. coli proteins. Inasmuch as the Swiss-Prot data base already contained 67% of the expected total of 4000 E. coli proteins, it is virtually certain that 96,000 varieties of hexapeptides containing at least one or another of the three missing tripeptides noted above shall be nonexistent in E. coli. Furthermore, the observation of missing tripeptides in the bakers' yeast proteins suggests that nonexistent hexapeptides shall be highly phylum specific. Because of the sample size, only a small fraction of the 20(6) varieties of hexapeptides were expected to be encountered in the present survey. Indeed, only 1.2-1.5% of the possible hexapeptides were found, and the average copy number of observed hexapeptides varied between 1.06 and 1.25. Nevertheless, 33 varieties of hexapeptides occurred in 102-169 copies among human proteins. Furthermore, 15 of the 33 varieties contained such rarely used residues as Tyr, His, Cys, and Trp.