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PubMed2000

Genetic diversity of the epiphytic bryophyte Leucodon sciuroides in formerly glaciated versus nonglaciated parts of Europe.

Twelve populations of the epiphytic bryophyte Leucodon sciuroides from three major regions representing formerly glaciated and nonglaciated regions of Europe were screened for polymorphisms at 15 putative isozyme loci. The populations clustered into three distinct groups consisting of: (i) a single population from Crete, representing a cryptic unknown taxon; (ii) four Scandinavian populations and two populations from northern Greece; and (iii) the remaining populations from mainland Greece and Crete. The Scandinavian populations were genetically depleted compared with most Greek populations, thus fitting the expectation of generally lower levels of variation in formerly glaciated areas. The transition zone between genetically diverse and depleted populations appears to be located through northern Greece, coinciding with the northern limit of the Mediterranean region. This indicates that genetic variation was lost in populations at the northern limit of glacial refugia. The two groups of populations fit a progenitor-derivative model. They also have contrasting reproductive strategies: the Mediterranean populations reproduce sexually, whereas the other populations propagate vegetatively. Epiphytic species, growing on substrates that are limited in space and time, appear to be especially vulnerable to loss of genetic variation. Lack of genetic variation and therefore low adaptability to increased levels of atmospheric pollution may explain why many epiphytic lichen and bryophytes, including L. sciuroides, are declining over much of Europe.

Electrophoresis, Starch Gel↗

PubMed1997

A major T cell determinant from the influenza virus hemagglutinin (HA) can be a cryptic self peptide in HA transgenic mice.

Transgenic (Tg) mice expressing the influenza virus PR8 hemagglutinin (PR8 HA) were infected with PR8 virus and analyzed for their ability to generate T cell responses to individual MHC class II-restricted T cell determinants from the HA. HAmemb and HAtrunc mice each express HA transgene mRNA in many tissues (including the thymus), but differ in the form and amount of the HA that is expressed: HAmemb mice express the entire viral HA as a membrane-bound neo-self antigen, whereas HAtrunc mice express lower levels of a truncated HA polypeptide. HAmemb mice were found to mediate efficient negative selection of autoreactive T cells directed to the major I-Ed-restricted and I-Ad-restricted determinants from the HA (designated S1 and S2 respectively). S1-specific T cell responses were similarly undetectable in PR8-infected HAtrunc mice. However, S2-specific T cells were only partially eliminated in HAtrunc mice; indeed, even though their frequency was reduced relative to non-Tg mice, S2-specific T cells still constituted a sizable population in PR8-infected HAtrunc mice. Moreover, the S2-specific T cells from HAtrunc and non-Tg mice appeared to be equally sensitive to stimulation with S2 peptide, and in each case utilized highly diverse T cell receptors to recognize S2-I-Ad. The findings demonstrate that an individual class II-restricted T cell determinant can be recognized as a cryptic self peptide during T cell repertoire formation and as an immunodominant peptide in the context of an anti-viral T cell response, providing a basis for the induction of autoreactive T cells by viruses containing homologs of self antigens.

Amino Acid Sequence↗

PubMed2006

Chromosomal variation and genome size support existence of cryptic species of Triatoma dimidiata with different epidemiological importance as Chagas disease vectors.

The wide geographical distribution of Triatoma dimidiata, one of the three major vectors of Chagas disease, ranges from Mexico to northern Peru. Since this species occupies a great diversity of artificial and natural ecotopes, its eradication is extremely difficult. In order to assist control efforts, we used chromosome analyses and DNA amount as taxonomic markers to study genetic variability in populations of T. dimidiata from Mexico, Guatemala, El Salvador and Colombia. We differentiated three groups or cytotypes defined by characteristic chromosome C-banding patterns and genome size measured by flow cytometry. The three cytotypes are restricted to different geographic locations. Cytotype 1 occurs in Mexico (excluding Yucatán), Guatemala (excluding Petén), El Salvador and Colombia. Cytotype 2 occurs in Yucatán and cytotype 3 occurs in Petén. Cytotype 1, commonly associated with domestic and peridomestic environments but also inhabiting sylvatic ecotopes, is the most widespread and with major epidemiological significance. In contrast, the Yucatán cytotype inhabits wild ecotopes but increasingly enters houses, while the Petén cytotype appears exclusively sylvatic. We suggest that these cytotypes represent cryptic species of T. dimidiata with different epidemiological relevance as Chagas disease vectors. Poor ability to colonize human dwellings, together with their restricted geographic distribution, indicate that the Yucatán and Petén putative species probably have much less epidemiological significance than cytotype 1. Thus, the genetic markers we describe are powerful tools to differentiate cryptic species in T. dimidiata with different epidemiological significance, contributing to planning the most effective control measures.

Animals↗

PubMed1995

Attenuation of Theiler's murine encephalomyelitis virus by modifications of the oligopyrimidine/AUG tandem, a host-dependent translational cis element.

A set of Theiler's murine encephalomyelitis virus mutants with engineered alterations in the conserved oligopyrimidine/AUG tandem (E. V. Pilipenko, A. P. Gmyl, S. V. Maslova, G. A. Belov, A. N. Sinyakov, M. Huang, T. D. K. Brown, and V. I. Agol, J. Mol. Biol. 241:398-414, 1994) were assayed for their growth potential in BHK-21 cells (as reflected in plaque size) and for neurovirulence upon intracerebral inoculation of mice. Tandem-destroying mutations, which included substitutions in the oligopyrimidine moiety and extended insertions into the oligopyrimidine/AUG spacer, exerted relatively little effect on the plaque size but ensured a high level of attenuation. The attenuated mutants exhibited remarkable genetic stability upon growth in BHK-21 cells. However, the brains of rare animals that developed symptoms after the inoculation with high doses of these mutants invariably contained pseudorevertants with the oligopyrimidine/AUG tandem restored by diverse deletions or an AUG-generating point mutation. The AUG moiety of the tandem in the revertant genomes was represented by either a cryptic codon or initiator codon. The results demonstrate that the tandem, while dispensable for the Theiler's murine encephalomyelitis virus growth in BHK-21 cells, is essential for neurovirulence in mice. Thus, the oligopyrimidine/AUG tandem is a host-dependent cis-acting control element that may be essential for virus replication under certain conditions. The functional activity of the tandem was retained when its oligopyrimidine or AUG moieties were made double stranded. A possible role of the tandem in the cap-independent internal initiation of translation on the picornavirus RNA templates is discussed.

Animals↗

PubMed2002

Rational design of a CD4 mimic that inhibits HIV-1 entry and exposes cryptic neutralization epitopes.

The conserved surfaces of the human immunodeficiency virus (HIV)-1 envelope involved in receptor binding represent potential targets for the development of entry inhibitors and neutralizing antibodies. Using structural information on a CD4-gp120-17b antibody complex, we have designed a 27-amino acid CD4 mimic, CD4M33, that presents optimal interactions with gp120 and binds to viral particles and diverse HIV-1 envelopes with CD4-like affinity. This mini-CD4 inhibits infection of both immortalized and primary cells by HIV-1, including primary patient isolates that are generally resistant to inhibition by soluble CD4. Furthermore, CD4M33 possesses functional properties of CD4, including the ability to unmask conserved neutralization epitopes of gp120 that are cryptic on the unbound glycoprotein. CD4M33 is a prototype of inhibitors of HIV-1 entry and, in complex with envelope proteins, a potential component of vaccine formulations, or a molecular target in phage display technology to develop broad-spectrum neutralizing antibodies.

CD4 Antigens↗

PubMed2005

Cryptic nature of a conserved, CD4-inducible V3 loop neutralization epitope in the native envelope glycoprotein oligomer of CCR5-restricted, but not CXCR4-using, primary human immunodeficiency virus type 1 strains.

The external subunit of the human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein (Env), gp120, contains conserved regions that mediate sequential interactions with two cellular receptor molecules, CD4 and a chemokine receptor, most commonly CCR5 or CXCR4. However, antibody accessibility to such regions is hindered by diverse protective mechanisms, including shielding by variable loops, conformational flexibility and extensive glycosylation. For the conserved neutralization epitopes hitherto described, antibody accessibility is reportedly unrelated to the viral coreceptor usage phenotype. Here, we characterize a novel, conserved gp120 neutralization epitope, recognized by a murine monoclonal antibody (MAb), D19, which is differentially accessible in the native HIV-1 Env according to its coreceptor specificity. The D19 epitope is contained within the third variable (V3) domain of gp120 and is distinct from those recognized by other V3-specific MAbs. To study the reactivity of MAb D19 with the native oligomeric Env, we generated a panel of PM1 cells persistently infected with diverse primary HIV-1 strains. The D19 epitope was conserved in the majority (23/29; 79.3%) of the subtype-B strains tested, as well as in selected strains from other genetic subtypes. Strikingly, in CCR5-restricted (R5) isolates, the D19 epitope was invariably cryptic, although it could be exposed by addition of soluble CD4 (sCD4); epitope masking was dependent on the native oligomeric structure of Env, since it was not observed with the corresponding monomeric gp120 molecules. By contrast, in CXCR4-using strains (X4 and R5X4), the epitope was constitutively accessible. In accordance with these results, R5 isolates were resistant to neutralization by MAb D19, becoming sensitive only upon addition of sCD4, whereas CXCR4-using isolates were neutralized regardless of the presence of sCD4. Other V3 epitopes examined did not display a similar divergence in accessibility based on coreceptor usage phenotype. These results provide the first evidence of a correlation between HIV-1 biological phenotype and neutralization sensitivity, raising the possibility that the in vivo evolution of HIV-1 coreceptor usage may be influenced by the selective pressure of specific host antibodies.

Amino Acid Sequence↗

PubMed1999

The importance of genetic diversity in livestock populations of the future.

Farm animal genetic diversity is required to meet current production needs in various environments, to allow sustained genetic improvement, and to facilitate rapid adaptation to changing breeding objectives. Production efficiency in pastoral species is closely tied to the use of diverse genetic types, but greater genetic uniformity has evolved in intensively raised species. In poultry, breeding decisions are directed by a few multinational companies and involve intense selection, the use of distinct production lines, and very large populations. In dairy cattle, the Holstein breed dominates production. Intensive sire selection is leading to relatively rapid inbreeding rates and raises questions about long-term effects of genetic drift. Key questions in management of farm animal genetic diversity involve the distribution of potentially useful quantitative trait locus alleles among global livestock breeds. Experiments with tomato, maize, and mice suggest that favorable alleles can exist in otherwise lowly productive stocks; this cryptic variation may potentially contribute to future selection response. Genetic improvement under relatively intense unidirectional selection may involve both increases in the frequency of favorable additive alleles as well as the progressive breakdown of homeostatic regulatory mechanisms established under the stabilizing selection that is characteristic of natural populations. Recombination among closely linked regulatory loci and new, potentially favorable mutations are possible sources of long-term genetic variation. A greater understanding of the potential that these alternative mechanisms have for supporting long-term genetic improvement and of genetic relationships among global livestock populations are priorities for managing farm animal genetic diversity.

Animal Husbandry↗

PubMed2003

A potential mechanism for cryptic female choice in a flour beetle.

In polyandrous mating systems, events occurring during copulation can alter the fate of the mating male's sperm. These events may exert selective pressures resulting in the evolution of diverse reproductive behaviours, morphologies and physiologies. This study investigates the role of male and female copulatory behaviours on sperm fate in the red flour beetle, Tribolium castaneum. I describe and quantify copulatory behaviours for mating pairs, and examine sperm fate by quantifying sperm transfer, sperm storage and second male sperm precedence. Whereas female quiescence during copulation and male leg rubbing during copulation together account for significant variation (26%) in sperm precedence, female copulatory quiescence alone provides information about the timing and numbers of sperm transferred. These experiments show that a female copulatory behaviour predicts sperm fate, and emphasize the value of studying variation in both male and female copulatory behaviours for understanding factors affecting sperm use.

Animals↗

PubMed2001

What causes the antiphospholipid syndrome?

The antiphospholipid syndrome (APS) is characterized by unpredictable, sporadic, thrombotic events. The cause of the thrombosis is probably multifactorial and may involve disparate effects of the autoantibodies associated with the syndrome, which are known to interfere with various protein regulators of hemostasis. An integrated theory of pathogenesis that accounts for the diversity of autoantibodies and their effects suggests that cellular inflammation or apoptosis within the vasculature may lead to oxidation or turnover in phospholipid membranes. Thus, normally cryptic, functionally important epitopes of phospholipid-binding proteins are subjected to increased exposure to immune surveillance.

Animals↗

PubMed2026

From sequence space to ecological function: microbiome-derived antimicrobial peptides as community effectors and therapeutic leads.

Antimicrobial peptide research has long centred on host defence molecules, yet microbiomes themselves encode a diverse and increasingly important repertoire of peptide-based antimicrobials. These microbiome-derived antimicrobial peptides include bacteriocins, ribosomally synthesised and post-translationally modified peptides, cryptic short open reading frame-encoded peptides, embedded antimicrobial regions within larger proteins, and selected peptide antibiotics recovered from human, animal, plant and environmental microbiomes. Recent advances in genome mining, metagenomics, and machine learning have greatly expanded the scale of discovery, moving the field from a handful of landmark exemplars to large candidate catalogues spanning the global microbiome. In the clearest cases, these molecules are not only anti-infective leads but ecological effectors: they mediate microbial competition, enforce colonisation resistance, and influence community structure within densely occupied niches. The present review synthesises the field across discovery classes, microbiome sources, ecological roles, and translational bottlenecks, emphasizing a central limitation of the field: candidate catalogues are expanding at extraordinary scale, while evidence for native expression, producer assignment, ecological function, and in vivo relevance remains limited for the vast majority of predicted molecules. Progress will depend on workflows that connect sequence level prediction to biological context through expression support, producer assignment, community level validation, and perturbation-based approaches that distinguish ecological association from causal function. Microbiome-derived antimicrobial peptides are best understood not only as promising therapeutic leads, but also as molecular mediators of microbial social life whose ecological origins are central to their interpretation and future application.

Microbiota↗

PubMed2000

Why do females mate multiply? A review of the genetic benefits.

The aim of this review is to consider the potential benefits that females may gain from mating more than once in a single reproductive cycle. The relationship between non-genetic and genetic benefits is briefly explored. We suggest that multiple mating for purely non-genetic benefits is unlikely as it invariably leads to the possibility of genetic benefits as well. We begin by briefly reviewing the main models for genetic benefits to mate choice, and the supporting evidence that choice can increase offspring performance and the sexual attractiveness of sons. We then explain how multiple mating can elevate offspring fitness by increasing the number of potential sires that compete, when this occurs in conjunction with mechanisms of paternity biasing that function in copula or post-copulation. We begin by identifying cases where females use pre-copulatory cues to identify mates prior to remating. In the simplest case, females remate because they identify a superior mate and 'trade up' genetically. The main evidence for this process comes from extra-pair copulation in birds. Second, we note other cases where pre-copulatory cues may be less reliable and females mate with several males to promote post-copulatory mechanisms that bias paternity. Although a distinction is drawn between sperm competition and cryptic female choice, we point out that the genetic benefits to polyandry in terms of producing more viable or sexually attractive offspring do not depend on the exact mechanism that leads to biased paternity. Post-copulatory mechanisms of paternity biasing may: (1) reduce genetic incompatibility between male and female genetic contributions to offspring; (2) increase offspring viability if there is a positive correlation between traits favoured post-copulation and those that improve performance under natural selection; (3) increase the ability of sons to gain paternity when they mate with polyandrous females. A third possibility is that genetic diversity among offspring is directly favoured. This can be due to bet-hedging (due to mate assessment errors or temporal fluctuations in the environment), beneficial interactions between less related siblings or the opportunity to preferentially fertilise eggs with sperm of a specific genotype drawn from a range of stored sperm depending on prevailing environmental conditions. We use case studies from the social insects to provide some concrete examples of the role of genetic diversity among progeny in elevating fitness. We conclude that post-copulatory mechanisms provide a more reliable way of selecting a genetically compatible mate than pre-copulatory mate choice. Some of the best evidence for cryptic female choice by sperm selection is due to selection of more compatible sperm. Two future areas of research seem likely to be profitable. First, more experimental evidence is needed demonstrating that multiple mating increases offspring fitness via genetic gains. Second, the role of multiple mating in promoting assortative fertilization and increasing reproductive isolation between populations may help us to understand sympatric speciation.

Animals↗

PubMed2024

Oceanic islands act as drivers for the genetic diversity of marine species: Cardita calyculata (Linnaeus, 1758) in the NE Atlantic as a case-study.

Geographic distribution, as well as evolutionary and biogeographic processes and patterns of marine invertebrate benthic species are strongly shaped by dispersal ability during the life cycle. Remote oceanic islands lie at the brink of complex biotic and abiotic interactions which have significantly influenced the biodiversity patterns we see today. The interaction between geological environmental change and taxon-specific dispersal modes can influence species evolutionary patterns, eventually delimiting species-specific biogeographic regions. In this study, we compare the population genetic patterns of the marine bivalve Cardita calyculata in the northeast Atlantic, discussing the role of Macaronesian islands during past climatic cycles. The genetic structure and diversity patterns were outlined based on SSR-GBAS loci of 165 individuals and on the mitochondrial COI marker of 22 individuals from the Canary Islands, Madeira, Azores and the Mediterranean. The highly structured genetic pattern found among regions and within archipelagos suggests the central role of oceanic islands in promoting the divergence of the species in both the NE Atlantic and the Mediterranean. The high degree of divergence in the COI dataset (> 7%) suggests the existence of potential cryptic speciation that needs to be further explored with a more comprehensive sampling. Such patterns are only congruent with a scenario where C. calyculata populations were maintained during glacial/interglacial cycles, supporting the role of the studied archipelagos as drivers of diversity for marine biota. We stress the importance of developing studies for species with various life history and dispersal modes. In such a way, a more profound understanding of the biogeographic and evolutionary significance of oceanic islands can catalyse directed conservation efforts, especially in the context of the ongoing climate crisis.

Animals↗

PubMed2006

Characterization of the mobilization determinants of pAN12, a small replicon from Rhodococcus erythropolis AN12.

Bacteria belonging to the Gram-positive actinomycete species, Rhodococcus erythropolis, are diverse not only in terms of metabolic potentials but the plasmids they encode. It was shown previously that the R. erythropolis AN12 genome harbors a 6.3kb cryptic plasmid called pAN12, which is a member of the pIJ101 family of plasmids. Here we show that pAN12 is conjugatively mobilizable into other rhodococcal strains. A series of plasmid deletion constructs were tested for loss of mobility to identify the pAN12 cis-acting conjugation requirement. In this way, an approximately 700bp region was found to be required for plasmid transmission. A small 61bp element within this region confers mobility to an otherwise non-mobilizable plasmid. Unlike pIJ101, which encodes all necessary factors for transfer, pAN12 mobility is dependent on the presence of an AN12 megaplasmid, pREA400.

Base Sequence↗

PubMed2003

Phylogeography of the harlequin beetle-riding pseudoscorpion and the rise of the Isthmus of Panamá.

Molecular and geological evidence indicates that the emergence of the Isthmus of Panamá influenced the historical biogeography of the Neotropics in a complex, staggered manner dating back at least 9 Myr bp. To assess the influence of Isthmus formation on the biogeography of the harlequin beetle-riding pseudoscorpion, Cordylochernes scorpioides, we analysed mitochondrial COI sequence data from 71 individuals from 13 locations in Panamá and northern South America. Parsimony and likelihood-based phylogenies identified deep divergence between South American and Panamanian clades. In contrast to low haplotype diversity in South America, the Panamanian Cordylochernes clade is comprised of three highly divergent lineages: one clade consisting predominantly of individuals from central Panamá (PAN A), and two sister clades (PAN B1 and PAN B2) of western Panamanian pseudoscorpions. Breeding experiments demonstrated a strictly maternal mode of inheritance, indicating that our analyses were not confounded by nuclear-mitochondrial pseudogenes. Haplotype diversity is striking in western Atlantic Panamá, where all three Panamanian clades can occur in a single host tree. This sympatry points to the existence of a cryptic species hybrid zone in western Panamá, a conclusion supported by interclade crosses and coalescence-based migration rates. Molecular clock estimates yield a divergence time of approximately 3 Myr between the central and western Panamanian clades. Taken together, these results are consistent with a recent model in which a transitory proto-Isthmus enabled an early wave of colonization out of South America at the close of the Miocene, followed by sea level rise, inundation of the terrestrial corridor and then a second wave of colonization that occurred when the Isthmus was completed approximately 3 Myr bp.

Animal Migration↗

PubMed2005

Placing the Floridian marine genetic disjunction into a regional evolutionary context using the scorched mussel, Brachidontes exustus, species complex.

The well-documented Floridian Gulf/Atlantic marine genetic disjunction provides an influential example of presumed vicariant cladogenesis along a continental coastline for major elements of a diverse nearshore fauna. However, it is unclear if this disjunction represents a local anomaly for regionally distributed morphospecies, or if it is merely one of many such cryptic phylogenetic splits that underlay their assumed genetic cohesiveness. We aimed to place the previously characterized scorched mussel Gulf/Atlantic genetic disjunction into a regional phylogenetic perspective by incorporating genotypes of nominal conspecifics sampled throughout the Caribbean Basin as well as those of eastern Pacific potential geminate species. Our results show it to be one of multiple latent regional genetic disjunctions, involving five cryptic Caribbean species, that appear to be the product of a long history of regional cladogenesis. Disjunctions involving three stem lineages clearly predate formation of the Isthmus of Panama and of the Caribbean Sea, although four of the five cryptic species have within-basin sister relationships. Surprisingly, the Atlantic clade was also found to be widespread in the southern Caribbean, and ancestral demography calculations through time for Atlantic coast-specific genotypes are consistent with a northward range extension after the last glacial maximum. Our new data seriously undermine the hypothesis of a Floridian vicariant genesis and imply that the scorched mussel Gulf/Atlantic disjunction represents a case of geographic and temporal pseudocongruence. All five Caribbean Basin cryptic species exhibited an intriguing pattern of predominantly allopatric distribution characterized by distinct geographic areas of ecological dominance, often adjoining those of sister taxa. This pattern of distribution is consistent with allopatric speciation origins, coupled with restricted postspeciation range extensions. Several lines of indirect evidence favor the hypothesis that the predominantly allopatric distributions are maintained over evolutionary time scales, primarily by postrecruitment ecological filters rather than by oceanographic barriers to larval-mediated gene flow.

Animals↗

PubMed1985

Glycolipid antigens of human polymorphonuclear neutrophils and the inducible HL-60 myeloid leukemia line.

Glycolipid and cell surface carbohydrate antigens of human polymorphonuclear neutrophils (PMN) and of HL-60 myeloid leukemia cells were analyzed with a panel of defined, monoclonal anti-carbohydrate antibodies. Antigenicities of intact PMN, HL-60, and retinoic acid-induced HL-60 (r.a.-HL-60) were studied by flow cytofluorometry. These three cell populations displayed quantitative differences, some of which were induction dependent, in their expression of lactosyl, N-acetyllactosaminyl, Y-hapten (Fuc alpha 1----2Gal beta 1----4(Fuc alpha 1----3)GlcNAc beta 1----R), and sialosyl-X-hapten (SA alpha 2----3Gal beta 1----4(Fuc alpha 1----3)GlcNAc beta 1----R) specificities. Structures reactive with antibodies specific for long-chain mono-, and di- or tri- alpha 1----3 fucosylated lacto-series glycolipids were also detected. Glycosphingolipids purified from organic extracts of these cells were analyzed to seek information concerning the chemical basis for these surface antigenic differences, to assess the structural and antigenic diversity of PMN and HL-60 glycolipids, and to quantitate chemically and antigenically prominent glycolipids. Binding of monoclonal antibodies to thin-layer chromatograms demonstrated that each of the specificities on intact cells was carried by one or more distinct glycolipids. The abundance of immunoreactive glycolipids in the extracts paralleled the relative staining intensities of the intact cell populations. Several "cryptic" glycolipid antigens, including alpha 2----6 sialosylated structures enriched five- to 10-fold in PMN extracts, were not detected on intact cells. Lactosylceramide accounted for two-thirds of the approximately 1.5 X 10(9) glycolipid molecules contained in each PMN. The remaining glycolipid antigens appeared to include structurally diverse fucolipids, fucogangliosides, and neutral and sialosylated glycolipids with Gal beta 1----4GlcNAc beta 1----R terminal core structure. The abundance, diversity, and induction-dependent expression of these structures suggest that they may participate in PMN maturation and function.

Amino Sugars↗

PubMed2026

Comparative genomics reveals hidden biosynthetic diversity in Streptomyces spp. and metal-dependent regulatory features associated with untapped specialized metabolites.

The genus Streptomyces is one of the richest sources of bioactive natural products; however, a substantial proportion of its biosynthetic gene clusters (BGCs) remain cryptic and their metabolic products are unresolved. Advances in genome mining and computational prediction now enable comprehensive exploration of this hidden biosynthetic repertoire. In this study, whole-genome sequencing and comparative genomic analyses were performed on three three newly isolated Streptomyces strains to evaluate their specialized metabolic potential. Genome assemblies were annotated and systematically analyzed using antiSMASH, DeepBGC, GECCO, and PRISM to identify, cross-validate, and functionally characterize BGCs while predicting their associated secondary metabolite scaffolds. Taxonomic analyses based on Average Nucleotide Identity (ANI), phylogenomics, and BLAST identified the isolates as Streptomyces thinghirensis, Streptomyces novocaesareae, and Streptomyces griseorubens. Applying the consensus framework across the three Streptomyces genomes yielded 43 cryptic BGCs, lacking close similarity to reference BGCs in the MIBiG database, of which 26 were classified as HIGH, 10 as MEDIUM, and 7 as LOW confidence. Notably, numerous BGCs exhibited low abundance to characterized reference clusters, indicating a high potential for previously undescribed biosynthetic pathways and novel metabolite scaffolds. Comparative analyses further revealed strain-specific biosynthetic architectures together with putative metal-responsive regulatory systems; Fur, Zur, and Nur, which were frequently associated with specialized metabolite biosynthetic loci. Collectively, these findings demonstrate the effectiveness of integrated genome-mining strategies for prioritizing cryptic biosynthetic gene clusters and highlight the remarkable biosynthetic potential of newly identified Streptomyces isolates as a source of novel natural products.

comparative genomics↗

PubMed1997

Dominant TCRB-V-J chain usage and clonal expansion of sarcoma-reactive CD4+ HLA-DR-restricted T cells suggest a limited set of immunodominant sarcoma antigens.

Tumor-reactive CD4+ T cells have been isolated from tumor patients, and their specifity but not T-cell receptor (TCR) repertoire has been analyzed. Since we have described CD4+ sarcoma-reactive T-cell clones, we now sought to determine whether the TCR repertoire of these clones provides information on the spectrum of recognized sarcoma antigens. We analyzed the TCR beta (TCRB) chain repertoire of 19 CD4+ HLA-DR-restricted T-cell clones reactive with the autologous sarcoma cell line MZ-MES-1, with HLA-DR-matched tumor cell lines of different tissue origins and B-cell blasts. We identified 7 different clonotypes, which used a limited set of TCRBV and TCRBJ segments. Although the CDR3 of the different clonotypes was diverse, repeated restimulation with sarcoma cells led to a monoclonal expansion of T cells with particular TCR clonotypes in 5/6 mixed lymphocyte tumor cell cultures (MLTC). One clonotype was found in 2 independent MLTC experiments. Sarcoma-reactive T cells were demonstrated in patient tumor-infiltrating lymphocytes (TIL) and peripheral blood mononuclear cells (PBMC) by clonotypic PCR. Our results indicate a limited number of immunodominant antigens expressed by the sarcoma cells. The junctional diversity of the TCR clonotypes shows that these antigens did not lead to extensive negative thymic selection as classical autoantigens would have. Therefore, the recognized antigens might represent cryptic autoantigens related to cellular transformation or proliferation.

Antigens, Neoplasm↗