Peptidase Loci Research Articles

CA/C1 peptidases of the malaria parasites Plasmodium falciparum and P. berghei and their mammalian hosts – a bioinformatical analysis

In genome-wide screens we studied CA/C1 peptidases of malaria-causing plasmodia and their hosts (man and mouse). For Plasmodium falciparum and P. berghei, several new CA/C1 peptidase genes encoding proteases of the L- and B-family with specific promoter modules were identified. In addition, two new human CA/C1 peptidase loci and one new mouse gene locus were found; otherwise, the sets of CA/C1 peptidase genes in man and mouse seem to be complete now. In each species studied there is a multitude of CA/C1 peptidases with lysosomal localization signals and partial functional overlap according to similar but subfamily-specific structures. Individual target structures in plasmodia include residues specifically different in CA/C1 peptidase subsite 2. This is of medical interest considering CA/C1 peptidase inhibition for chemotherapy in malaria, malignancies and other diseases. Promoter structures and mRNA regulation differ widely among CA/C1 peptidase subfamilies and between mammals and plasmodia. We characterized promoter modules conserved in mouse and man for the CA/C1 peptidase families B and L (with the L-like subfamily, F-like subfamily and mouse-specific J-like subfamily). RNA motif searches revealed conserved regulatory elements such as GAIT elements; plasmodial CA/C1 peptidase mRNA elements include ARE elements and mammalian mRNAs contain 15-lox DICE elements.

Characterization of urease-positive thermophilic Campylobacter subspecies by multilocus enzyme electrophoresis typing.

Thirty-one urease-positive thermophilic Campylobacter (UPTC) isolates, including three reference strains (NCTC12892, NCTC12895 and NCTC12896), and three Campylobacter lari isolates, which were isolated from several countries and sources, were compared genotypically by using multilocus enzyme electrophoresis (MLEE). We examined allelic variation around seven enzyme loci, including the adenylate kinase, alkaline phosphatase, catalase, fumarase, malic enzyme, malate dehydrogenase, and L-phenylalanyl-L-leucine peptidase loci. MLEE typing revealed the presence of 23 different electrophoretic types (ETs) among the 31 UPTC isolates, and 14 isolates shared six electrophoretic profiles. Three different ETs were identified for the three C. lari isolates examined, and no ETs were shared by UPTC and C. lari isolates. Quantitative analyses were subsequently performed by using allelic variation data, and the results demonstrated that the mean genetic diversity was 0.655. In conclusion, MLEE demonstrated that the UPTC isolates examined are genetically hypervariable and form a cluster separate from the C. lari cluster.

Characterisation of Isolates of Phytophthora infestans From Hungary

A total of 36 single-lesion isolates were collected from 9 crops of potato and 13 of tomato in different regions of Hungary in the past decade, particularly in 1998. These were analysed for mating type, sensitivity to metalaxyl, allozyme genotype at glucose-6-phosphate isomerase and peptidase loci and genotype at 24 loci detected using the multilocus RFLP probe RG57. The ratios of the mating types A1 to A2 were 8 : 9 and 4 : 15 among isolates recovered from potato and tomato, respectively. Resistance to metalaxyl was found more frequently among isolates from potato and in the A1 mating type. The populations were not clearly differentiated on the basis of host origin. All isolates were homozygous (100/100) at the locus for glucose-6-phosphate isomerase. Unlike in other European countries, the most common peptidase allele was 96. Genotypes at the peptidase locus were 96/96 (50%), 96/100 (27.7%) and 100/100 (16.6%). In addition, one isolate from 1993 and another from 1998, were defined as 83/96, a genotype that had not been described elsewhere. The 18 RG57 fingerprints that were observed among 36 isolates, with one exception, seem to be unique to Europe. On the basis of combined genotypic traits, 20 multilocus genotypes were designated. These data, which reveal a remarkable variability with unique genotypes of the late blight pathogen, suggest that migration and sexual and/or asexual recombination have a role in the recent evolution of the pathogen in Hungary.

Spatial Analysis of Phytophthora infestans Genotypes and Late Blight Severity on Tomato and Potato in the Del Fuerte Valley Using Geostatistics and Geographic Information Systems

ABSTRACT Genetic structure of Phytophthora infestans, the causal agent of potato and tomato late blight, was analyzed spatially in a mixed potato and tomato production area in the Del Fuerte Valley, Sinaloa, Mexico. Isolates of P. infestans were characterized by mating type, allozyme analysis at the glucose-6-phosphate isomerase and peptidase loci, restriction fragment length polymorphism with probe RG57, metalaxyl sensitivity, and aggressiveness to tomato and potato. Spatial patterns of P. infestans genotypes were analyzed by geographical information systems and geo-statistics during the seasons of 1994-95, 1995-96, and 1996-97. Spatial analysis of the genetic structure of P. infestans indicates that geographic substructuring of this pathogen occurs in this area. Maps displaying the probabilities of occurrence of mating types and genotypes of P. infestans, and of disease severity at a regional scale, were presented. Some genotypes that exhibited differences in epidemiologically important features such as metalaxyl sensitivity and aggressiveness to tomato and potato had a restricted spread and were localized in isolated areas. Analysis of late blight severity showed recurring patterns, such as the earliest onset of the disease in the area where both potato and tomato were growing, strengthening the hypothesis that infected potato tubers are the main source of primary inoculum. The information that geostatistical analysis provides might help improve management programs for late blight in the Del Fuerte Valley.

Genotypic Analysis of Russian Isolates of Phytophthora infestans from the Moscow Region, Siberia and Far East

Phytophthora infestans samples were collected during 1997 and 1998 at multiple sites in Russia from Sakhalin Island in the Far East across Siberia (nine sites, 160 isolates) to the Moscow region (four sites, 325 isolates). In addition, 12 isolates that were obtained previously were included. All isolates were analysed for mating type, and sensitivity to metalaxyl. Isolates from within any of the nine sites outside of the Moscow region were monomorphic for mating type and nearly monomorphic for metalaxyl resistance. In contrast, both A1 and A2 isolates were detected in the Moscow region, and these isolates were also polymorphic for metalaxyl resistance. In two sites in Siberia only A2 mating type strains were detected, in the other six sites in Siberia and in Sakahlin Island, only A1 mating types were detected. A subset of isolates (n=191) was also analysed for pathotype (virulence to 10 R‐genes, each in a distinct differential genotype). All isolates were highly complex (mean number of virulences approximately 8.4 of a maximum number of 10). All isolates (n=43) from Sakahlin Island were virulent to all 10 of the R‐genes tested. A further subset of isolates (n=70, including 12 isolates collected before 1997) was analysed for genotype at the Glucose‐ 6‐phosphate isomerase and Peptidase loci, mtDNA haplotypes, and RFLP pattern using the RG57 probe. The US‐1 clonal lineage (previously dominant) was not detected in the 1997–98 sample. The populations of P. infestans near Moscow in 1997 and 1998 was highly diverse with 15 unique genotypes (including both mating types) among a sample of 18 isolates. In contrast, the populations of P. infestans in Siberia had limited diversity, with only three multilocus genotypes detected and most populations were dominated by the SIB‐1 clonal lineage. This lineage accounted for 31 of the 39 strains collected in Siberia that were assayed for multilocus genotype.

Temporal and Spatial Patterns of Genetic Structure of Phytophthora infestans from Tomato and Potato in the Del Fuerte Valley

ABSTRACT The temporal and spatial patterns of Phytophthora infestans population genetic structure were analyzed in the Del Fuerte Valley, Sinaloa, Mexico, during the crop seasons of 1994 to 1995, 1995 to 1996, and 1996 to 1997 by geographical information systems. Isolates of P. infestans were obtained from infected tissue of tomato and potato collected from two areas: (i) where both potatoes and tomatoes are grown, and (ii) where only tomatoes are grown. The isolates were characterized by mating type, allozymes at the glucose-6-phosphate isomerase and peptidase loci, restriction fragment length polymorphism (RFLP) fingerprint with probe RG57, metalaxyl sensitivity, and aggressiveness to tomato and potato. The results suggest presence of an asexual population with frequent immigrations from outside the valley. There was a shift of mating type in the population from predominantly A2 to completely A1 in this period. The co-occurrence of mating types was restricted to very few fields in the area around Los Mochis where tomato and potato crops are grown. Genotype variation based on allozyme analysis and mating type was low with only one genotype affecting both crops each year. The genotypes affecting both crops were the only genotypes highly aggressive to both tomato and potato in laboratory aggressiveness tests and the only genotypes widespread on both the tomato and potato crops in the valley each year. These predominant genotypes were highly resistant to the fungicide metalaxyl. Data on metalaxyl sensitivity indicate that allozyme analysis can discriminate between sensitive and resistant isolates in the Del Fuerte Valley. RFLP analysis with the probe RG57 gives further discrimination of genotypes within an allozyme genotype. In the 1995 to 1996 season, four different RFLP genotypes were found within an allozyme genotype. However, there were five other dilocus allozyme genotypes that could not be further split by RFLP analysis in 1995 to 1996 and 1996 to 1997 seasons. Spatial analysis of genotypes suggests that each season individual fields near Los Mochis became infected with one or more genotypes, but only a single genotype, aggressive on both potato and tomato, occurred south and east to the Guasave area.

Distribution of Phytophthora infestans Populationsin Seven Asian Countries.

The mating type, allozyme genotypes of malic enzyme, glucose-6-phosphate isomerase and peptidase loci, and metalaxyl sensitivity of 336 Phytophthora infestans isolates collected in Korea, India, Taiwan, Indonesia, Thailand, Nepal, and China between 1992 and 1997 were determined. Only A1 mating type isolates were detected in India and Taiwan, and only A2 isolates in Korea and Indonesia, while both mating type isolates were detected in Thailand, Nepal, and China. The isolates from Korea, India, Taiwan, and Indonesia had a single allozyme genotype respectively, while the isolates from Thailand, Nepal, and China had two or three allozyme genotypes. Isolates that were highly resistant to metalaxyl were found in Korea, Indonesia, and China. All of the isolates from Taiwan and India, and some of the isolates from Thailand, Nepal, and northern and southern areas of China, belonged to the old population of P. infestans, which was predominant worldwide until the appearance of A2 isolates outside central Mexico. Some of the isolates from Thailand and Nepal were from new populations that have been discovered since the appearance of A2 isolates outside central Mexico. All of the isolates from Korea and Indonesia and most of the isolates from China belonged to two specific populations, which have been rarely detected elsewhere. The occurrence of these separate populations in Asia suggests that they followed a different migration pathway, or that they are better adapted to Asian conditions than to those elsewhere in the world.

High levels of gene flow in the surf bivalve Donax deltoides (Bivalvia: Donacidae) on the east coast of Australia

We surveyed patterns of allelic variation within twelve samples of the pipi Donax deltoides Lamarck from beaches separated by up to 1200 km but connected to varying degrees by the East Australian Current. We used these data to test the prediction that the irregular patterns of water movement would cause genetic differentiation in pipis, so that there would be more genetic variation within and among the more southern regions than the northern regions. We found that six loci were at least moderately variable within all samples, and there were no clear geographic patterns in allelic frequencies. In general, genotype frequencies within samples were consistent with predictions for an outcrossed, sexually reproducing species, and we detected no evidence of population subdivision. Within samples, with the exception of the peptidase loci, single-locus genotype frequencies were in close agreement with expectations for Hardy–Weinberg equilibrium. We observed no significant linkage disequilibrium for any pairwise comparison of loci in any sample. Our hierarchical analysis of genetic variation revealed little variation among all samples (Fst = 0.009). Loci showed consistently low levels of subdivision (Fst from 0.003 to 0.018). We found almost no variation among the four geographic regions sampled (Frt = 0.001). All variation was therefore attributable to variation among samples within regions (Fsr = 0.010). These data imply that larvae are moving between regions and that levels of present or recent gene flow are high, and support the conclusions of other studies which have inferred widespread gene flow for animals dispersing via planktonic, outcrossed larvae in parts of this region. This implies that the East Australian Current is sufficient to produce strong larval connections despite its intermittent nature. If existing levels of population subdivision reflect current levels of gene flow, then these data imply that D. deltoides represents a single fishery on the east coast of Australia.

Genetic Evidence for Undetected Alleles and Unexpected Parentage in the Gray-Breasted Jay

We performed protein electrophoresis to detect multiple parentage in broods of the Gray-breasted Jay (Aphelocoma ultramarina), a plural breeder that has been studied since 1969 in southeastern Arizona. We analyzed data from 43 nests (142 nestlings) for which we had blood, muscle, or feather samples from the nestlings and from at least one of the primary adults at a nest. Detection of multiple parentage was complicated by the apparent existence of an undetected (either null or masked) allele at the leu-gly-gly peptidase locus. The undetected allele resulted in offspring with single-banded phenotypes that were inconsistent with the phenotypes of adults with different single-banded phenotypes, assuming simple Mendelian inheritance. Including inconsistencies due to the undetected allele, we detected inconsistencies at 14 nests (33% of total), involving 29 nestlings (20%). We estimate that inconsistencies at seven nests (16%), involving 13 nestlings (8%) were due to causes other than the undetected allele. Inconsistencies at three nests were due to multiple parentage within broods, as the nestlings had double-banded phenotypes. The genetic data for these three nests did not allow us to distinguish between multiple paternity and multiple maternity. Data on clutch size and behavior indicated that multiple paternity was most likely. Inconsistencies at three nests in which nestlings had single-banded phenotypes were likely due to multiple paternity. Inconsistencies at five nests were most parsimoniously explained by an undetected allele present in three generations of one lineage and inconsistencies at two additional nests were likely due to an undetected allele. We attributed inconsistencies at one nest to nest usurpation. We argue that some females may gain a phenotypic benefit from mating with more than one male. Males that mated with a female may be more likely to feed her on the nest and to feed her nestlings

Phenotypes of Phytophthora infestans collected in England and Wales from 1985 to 1988: mating type, response to metalaxyl and isoenzyme analysis

In a survey of 1864 isolates derived from samples of Phytophthora infestans obtained from potato and tomato collected in England and Wales between 1985 and 1988, the A2 mating type was identified in approximately 10% of samples. There was no evidence for an overall increase in the frequency of the A2 mating type over this period. In agar culture, A2 isolates exhibited a distinct lumpy‐colony morphology. Lumps were made up of intensely dichotomously branched hyphae. The incidence of resistance to metalaxyl among samples increased from 41 to 60% between 1986 and 1988. Some of the A2 isolates were resistant to metalaxyl and like other A2 isolates gave rise to progeny from in vitro matings with Al isolates. Except in one case, Al and A2 isolates were uniformly homozygous at an isoenzyme locus for glucosephosphate isomerase but isolates exhibited some variation at a peptidase locus. The source of the A2 isolates could not be established from these data.

Inheritance and Expression of Two Peptidases in the Wallaroo, Macropus rohustus (Gould)

The formal genetics of two peptidase loci in M. robustus are presented. Both loci are autosomal but do not appear to be located on the same chromosome pair. Alleles at both loci are codominantly expressed in neonates, pouch young and adults. The application of autosomal loci segregating for three or more alleles in studies of embryonic gene expression is discussed.

Dipeptidase-A: A polymorphic locus in Drosophila melanogaster

Dipeptidase A (Dip-A), a new peptidase locus in Drosophila melanogaster, is located on the second chromosome at map position 55.2 and in the 41A-B; 42A2-3 interval in the salivary gland chromosomes. Three alleles are reported. In the Carpenter, North Carolina population the allele frequencies are: Dip-A 6 (fastest)=0.064; Dip-A 4 (intermediate)=0.920; and Dip-A 2 (slowest)=0.015.

Linkage studies on Peptidases A, B, C and D in man

SUMMARYLinkage data obtained from studies on families segregating for electrophoretic variants of red cell peptidases A, b, C, D, are presented in the form of lod scores and of recombinants and non‐recombinants. No significant linkages were found, but ‘hints’ of linkage between pep B and Gm, between Pep C and Rh, and between Pep D, Lu and Secretor are discusse. There appears to be no close linkage between the four peptidase loci A, B, C, and D.