scholarly journals Beyond the reach of homology: successive computational filters find yeast pheromone genes

2021 ◽  
Author(s):  
Sriram Srikant ◽  
Rachelle Gaudet ◽  
Andrew W Murray
Keyword(s):  
Proteolytic Processing ◽  
Mating Types ◽  
Computational Pipeline ◽  
Gene Encoding ◽  
Closely Related Species ◽  
Homologous Sequences ◽  
Manual Curation ◽  
Fungal Genomes ◽  
Strong Candidate ◽  
Time Required

The mating of fungi depends on pheromones that mediate communication between two mating types. Most species use short peptides as pheromones, which are either unmodified (e.g., α-factor in Saccharomyces cerevisiae) or C-terminally farnesylated (e.g., a-factor in S. cerevisiae). Peptide pheromones have been found by genetics or biochemistry in small number of fungi, but their short sequences and modest conservation make it impossible to detect homologous sequences in most species. To overcome this problem, we used a four-step computational pipeline to identify candidate a-factor genes in sequenced genomes of the Saccharomycotina, the fungal clade that contains most of the yeasts: we require that candidate genes have a C-terminal prenylation motif, are fewer than 100 amino acids long, contain a proteolytic processing motif upstream of the potential mature pheromone sequence, and that closely related species contain highly conserved homologs of the potential mature pheromone sequence. Additional manual curation exploits the observation that many species carry more than one a-factor gene, encoding identical or nearly identical pheromones. From 332 fungal genomes, we identified strong candidate pheromone genes in 238 genomes, covering 13 clades that are separated from each other by at least 100 million years, the time required for evolution to remove detectable sequence homology. For one small clade, the Yarrowia, we demonstrated that our algorithm found the a-factor genes: deleting all four related genes in the a-mating type of Yarrowia lipolytica prevents mating.

Products, genetic linkage and limb patterning activity of a murine hedgehog gene

Development ◽  
1994 ◽  
Vol 120 (11) ◽  
pp. 3339-3353 ◽  
Author(s):  
D.T. Chang ◽  
A. Lopez ◽  
D.P. von Kessler ◽  
C. Chiang ◽  
B.K. Simandl ◽  
...  
Keyword(s):  
Limb Development ◽  
Genetic Linkage ◽  
Pcr Primers ◽  
Amino Acid Identity ◽  
Protein Product ◽  
Proteolytic Processing ◽  
Limb Bud ◽  
Gene Encoding ◽  
Mouse Limb ◽  
Drosophila Embryos

The hedgehog (hh) segmentation gene of Drosophila melanogaster encodes a secreted signaling protein that functions in the patterning of larval and adult structures. Using low stringency hybridization and degenerate PCR primers, we have isolated complete or partial hh-like sequences from a range of invertebrate species including other insects, leech and sea urchin. We have also isolated three mouse and two human DNA fragments encoding distinct hh-like sequences. Our studies have focused upon Hhg-1, a mouse gene encoding a protein with 46% amino acid identity to hh. The Hhg-1 gene, which corresponds to the previously described vhh-1 or sonic class, is expressed in the notochord, ventral neural tube, lung bud, hindgut and posterior margin of the limb bud in developing mouse embryos. By segregation analysis the Hhg-1 gene has been localized to a region in proximal chromosome 5, where two mutations affecting mouse limb development previously have been mapped. In Drosophila embryos, ubiquitous expression of the Hhg-1 gene yields effects upon gene expression and cuticle pattern similar to those observed for the Drosophila hh gene. We also find that cultured quail cells transfected with a Hhg-1 expression construct can induce digit duplications when grafted to anterior or mid-distal but not posterior borders within the developing chick limb; more proximal limb element duplications are induced exclusively by mid-distal grafts. Both in transgenic Drosophila embryos and in transfected quail cells, the Hhg-1 protein product is cleaved to yield two stable fragments from a single larger precursor. The significance of Hhg-1 genetic linkage, patterning activity and proteolytic processing in Drosophila and chick embryos is discussed.

scholarly journals Random sampling of the Central European bat fauna reveals the existence of numerous hitherto unknown adenoviruses

2015 ◽  
Vol 63 (4) ◽  
pp. 508-525 ◽  
Author(s):  
Márton Z. Vidovszky ◽  
Claudia Kohl ◽  
Sándor Boldogh ◽  
Tamás Görföl ◽  
Gudrun Wibbelt ◽  
...  
Keyword(s):  
Rectal Swab ◽  
Polymerase Gene ◽  
Internal Organs ◽  
Gene Encoding ◽  
Closely Related Species ◽  
Central European ◽  
Extant Species ◽  
High Prevalence ◽  
Pcr Products ◽  
And Migration

From over 1250 extant species of the order Chiroptera, 25 and 28 are known to occur in Germany and Hungary, respectively. Close to 350 samples originating from 28 bat species (17 from Germany, 27 from Hungary) were screened for the presence of adenoviruses (AdVs) using a nested PCR that targets the DNA polymerase gene of AdVs. An additional PCR was designed and applied to amplify a fragment from the gene encoding the IVa2 protein of mastadenoviruses. All German samples originated from organs of bats found moribund or dead. The Hungarian samples were excrements collected from colonies of known bat species, throat or rectal swab samples, taken from live individuals that had been captured for faunistic surveys and migration studies, as well as internal organs of dead specimens. Overall, 51 samples (14.73%) were found positive. We detected 28 seemingly novel and six previously described bat AdVs by sequencing the PCR products. The positivity rate was the highest among the guano samples of bat colonies. In phylogeny reconstructions, the AdVs detected in bats clustered roughly, but not perfectly, according to the hosts’ families (Vespertilionidae, Rhinolophidae, Hipposideridae, Phyllostomidae and Pteropodidae). In a few cases, identical sequences were derived from animals of closely related species. On the other hand, some bat species proved to harbour more than one type of AdV. The high prevalence of infection and the large number of chiropteran species worldwide make us hypothesise that hundreds of different yet unknown AdV types might circulate in bats.

scholarly journals Phylogenetic analysis of genomic islands in closely-related species belonging to Sinorhizobium sp.

2020 ◽  
Author(s):  
M. E. Vladimirova ◽  
V. S. Muntyan ◽  
A. S. Saksaganskaya ◽  
B. V. Simarov ◽  
M. L. Roumiantseva
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Related Species ◽  
Genomic Islands ◽  
Closely Related Species ◽  
Homologous Sequences

Genomic islands of closely related S. meliloti and S. medicae species were evaluated and homologous sequences were identified; it has been suggested that horizontal gene transfer occurs at homologous tRNA sites.

scholarly journals The Ras-specific exchange factors mouse Sos1 (mSos1) and mSos2 are regulated differently: mSos2 contains ubiquitination signals absent in mSos1.

1997 ◽  
Vol 17 (12) ◽  
pp. 7132-7138 ◽  
Author(s):  
K H Nielsen ◽  
A G Papageorge ◽  
W C Vass ◽  
B M Willumsen ◽  
D R Lowy
Keyword(s):  
Growth Conditions ◽  
Chimeric Proteins ◽  
3T3 Cells ◽  
Gene Encoding ◽  
Homologous Sequences ◽  
C Terminus ◽  
Reticulocyte Lysate ◽  
Nih 3T3 ◽  
Nih 3T3 Cells

We have compared aspects of the mouse sos1 (msos1) and msos2 genes, which encode widely expressed, closely related Ras-specific exchange factors. Although an msos1 plasmid did not induce phenotypic changes in NIH 3T3 cells, addition of a 15-codon myristoylation signal to its 5' end enabled the resulting plasmid, myr-sos1, to induce approximately one-half as many foci of transformed cells as a v-H-ras control. By contrast, an isogenic myr-sos2 plasmid, which was made by fusing the first 102 codons from myr-sos1 at homologous sequences to an intact msos2 cDNA, did not induce focal transformation directly, although it could form foci in cooperation with c-H-ras. Pulse-chase experiments indicated that the half-life of Sos1 in NIH 3T3 cells was greater than 18 h, while that of Sos2 was less than 3 h. While in vitro-translated Sos1 was stable in a rabbit reticulocyte lysate, Sos2 was degraded in the lysate, as were each of two reciprocal chimeric Sos1-Sos2 proteins, albeit at a slower rate. In the lysate, Sos2 and the two chimeric proteins could be stabilized by ATPgammaS. Unlike Sos1, Sos2 was specifically immunoprecipitated by antiubiquitin antibodies. In a myristoylated version, the chimeric gene encoding Sos2 at its C terminus made a stable protein in NIH 3T3 cells and induced focal transformation almost as efficiently as myr-msos1, while the myristoylated protein encoded by the other chimera was unstable and defective in the transformation assay. We conclude that mSos2 is much less stable than mSos1 and is degraded by a ubiquitin-dependent process. A second mSos2 degradation signal, mapped to the C terminus in the reticulocyte lysate, does not seem to function under the growth conditions of the NIH 3T3 cells.

Movement of Food in the Gut of Some Adult Stored Grain Beetles

1958 ◽  
Vol 90 (4) ◽  
pp. 202-212 ◽  
Author(s):  
R. N. Sinha
Keyword(s):  
Alimentary Canal ◽  
American Cockroach ◽  
Stored Grain ◽  
Closely Related Species ◽  
Anatomical Structures ◽  
Grain Beetles ◽  
The Difference ◽  
Time Required ◽  
Starch Paste ◽  
Different Parts

The time required for passage of food through various segments of the alimentary canal is important in understanding the process of digestion in insects. Abbott (1926) gave some information on this subject in connection with his study of the physiology of digestion in the Australian roach, Perqlaneta australasiae Fab. Snipes and Tauber (1937), have recorded the time required for passage and ejection of one type of food in the American cockroach, P. americana L. Later Day and Powning (1949) studied the time taken for starch paste to reach different parts of the alimentary canal of the German cockroach, Blattella germmica (L.). But any information in this respect seems to be lacking in numerous species of insects other than the cockroach. This study was undertaken to determine the time required to reach various points of the gut of small stored grain beetles, to find out the difference in the time requirement between two closely related species living on same diet and between large and small insects. Investigations were also made to locate the region of mixing in the gut of two subsequent meals, to understand the significance of certain anatomical structures in the gut in relation to the movement of food. The adult beetles used in these experiments were, Tribolium confusum Duv., T. castaneum Herbst (Fam. Tenebrionidae), Oryzaephilus surinamensis (L.), O. mercator (Fauval) and Laemophloeus pusilloides Steel and Howe (Fam. Cucujidae).

scholarly journals Three new species of soil-inhabiting Trichoderma from southwest China

MycoKeys ◽  
2018 ◽  
Vol 44 ◽  
pp. 63-80 ◽  
Author(s):  
Min Qiao ◽  
Xing Du ◽  
Zhe Zhang ◽  
JianPing Xu ◽  
ZenFen Yu
Keyword(s):  
New Species ◽  
Dna Sequences ◽  
Elongation Factor ◽  
Gene Encoding ◽  
Translation Elongation ◽  
Closely Related Species ◽  
Encoding Gene ◽  
Three New Species ◽  
Elongation Factor 1 ◽  
Nuclear Rna Polymerase

Fungi in the genus Trichoderma are widely distributed in China, including in Yunnan province. In this study, we report three new soil-inhabiting species in Trichoderma, named as T.kunmingense, T.speciosum and T.zeloharzianum. Their colony and mycelial morphology, including features of asexual states, were described. For each species, their DNA sequences were obtained from three loci, the internal transcribed spacer (ITS) regions of the ribosomal DNA, the translation elongation factor 1-α encoding gene (tef1) and the gene encoding the second largest nuclear RNA polymerase subunit (rpb2). Our analyses indicated that the three new species showed consistent divergence amongst each other and from other known and closely related species. Amongst the three, T.speciosum and T.kunmingense belong to the Viride Clade. Specifically, T.speciosum is related to three species – T.hispanicum, T.samuelsii and T.junci and is characterised by tree-like conidiophores, generally paired branches, curved terminal branches, spindly to fusiform phialides and subglobose to globose conidia. In contrast, T.kunmingense morphologically resembles T.asperellum and T.yunnanense and is distinguished by its pyramidal conidiophores, ampulliform to tapered phialides, discrete branches and ovoidal, occasionally ellipsoid, smooth-walled conidia. The third new species, T.zeloharzianum, is a new member of the Harzianum Clade and is closely associated with T.harzianum, T.lixii and T.simmonsii but distinguished from them by having smaller, subglobose to globose, thin-walled conidia.

scholarly journals Rapid Detection of Colicin E9-Induced DNA Damage Using Escherichia coli Cells Carrying SOS Promoter-lux Fusions

2005 ◽  
Vol 187 (14) ◽  
pp. 4900-4907 ◽  
Author(s):  
Mireille Vankemmelbeke ◽  
Bryan Healy ◽  
Geoffrey R. Moore ◽  
Colin Kleanthous ◽  
Christopher N. Penfold ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Dna Damage ◽  
Structural Motif ◽  
Homing Endonucleases ◽  
Reporter System ◽  
Closely Related Species ◽  
E Coli ◽  
Double Stranded Dna ◽  
Time Required ◽  
Colicin E9

ABSTRACT ColE9 is a plasmid-encoded protein antibiotic produced by Escherichia coli and closely related species that kills E. coli cells expressing the BtuB receptor. The 15-kDa cytotoxic DNase domain of colicin E9 preferentially nicks double-stranded DNA at thymine bases and shares a common active-site structural motif with a variety of other nucleases, including the H-N-H homing endonucleases and the apoptotic CAD proteins of eukaryotes. Studies of the mechanism by which the DNase domain of ColE9 reaches the cytoplasm of E. coli cells are limited by the lack of a rapid, sensitive assay for the DNA damage that results. Here, we report the development of an SOS promoter-lux fusion reporter system for monitoring DNA damage in colicin-treated cells and illustrate the value of this reporter system in experiments that probe the mechanism and time required for the DNase domain of colicin E9 to reach the cytoplasm.

scholarly journals Premature Death in Podospora anserina: Sporadic Accumulation of the Deleted Mitochondrial Genome, Translational Parameters and Innocuity of the Mating Types

Genetics ◽  
1996 ◽  
Vol 144 (2) ◽  
pp. 541-555
Author(s):  
Véronique Contamine ◽  
Gael Lecellier ◽  
Leon Belcour ◽  
Marguerite Picard
Keyword(s):  
Mitochondrial Genome ◽  
Premature Death ◽  
Culture Conditions ◽  
Podospora Anserina ◽  
Mating Types ◽  
Gene Encoding ◽  
Type Locus ◽  
Linked Gene ◽  
A Site ◽  
Specific Deletion

Abstract The Podospora anserina premature death syndrome was described as early growth arrest caused by a site-specific deletion of the mitochondrial genome (mtDNA) and occurring in strains displaying the genotype AS1-4 mat−. The AS1-4 mutation lies in a gene encoding a cytosolic ribosomal protein, while mat− is one of the two forms (mat− and mat+) of the mating-type locus. Here we show that, depending on culture conditions, death due to the accumulation of the deleted mtDNA molecule can occur in the AS1-4 mat+ context and can be delayed in the AS1-4 mat− background. Furthermore, we show that premature death and the classical senescence process are mutually exclusive. Several approaches permit the identification of the mat-linked gene involved in the appearance of premature death. This gene, rmp, exhibits two natural alleles, rmp− linked to mat− and rmp+ linked to mat+. The first is probably functional while the second probably carries a nonsense mutation and is sporadically expressed through natural suppression. A model is proposed that emphasizes the roles played by the AS1-4 mutation, the rmp gene, and environmental conditions in the accumulation of the deleted mitochondrial genome characteristic of this syndrome.

PREPARATION OF PROTOPLASTS FROM STATIONARY PHASE CELLS OFSCHIZOSACCHAROMYCES POMBE

1971 ◽  
Vol 13 (4) ◽  
pp. 714-719 ◽  
Author(s):  
M. M. Shahin
Keyword(s):  
Stationary Phase ◽  
Schizosaccharomyces Pombe ◽  
Helix Pomatia ◽  
Mating Types ◽  
Protoplast Formation ◽  
Commercial Preparation ◽  
Wild Strains ◽  
Snail Helix Pomatia ◽  
Different Strains ◽  
Time Required

A high percentage of protoplasts was obtained from stationary phase cells of Schizosaccharomyces pombe by using the commercial preparation Helicase, obtained from the snail Helix pomatia. This was achieved with five different strains of S. pombe: the wild strains of three different mating types, 975h+and 972h−(heterothalic), and 968h90(homothalic); one adenine auxotroph (adn-3h+); and a radiation-sensitive strain (UVS-1h−). In all five strains the time required for protoplast formation increased greatly as soon as the culture outgrew the logarithmic and entered the stationary phase. Cells from the same logarithmic or stationary phase also showed different susceptibility to attack by Helicase. However, it is interesting to note that no protoplast formation was achieved from stationary phase cells of the three adenine-requiring strains: adn-7, 407h−, adn7-50//la UVS1h−and adn-7, adn-1.

scholarly journals CaProDH2-mediated modulation of proline metabolism confers tolerance to Ascochyta in chickpea under drought

2021 ◽  
Author(s):  
Mahesh Patil ◽  
Prachi Pandey ◽  
Vadivelmurugan Irrulappan ◽  
Anuradha Singh ◽  
Praveen Verma ◽  
...  
Keyword(s):  
Plant Defense ◽  
Defense Mechanisms ◽  
Defense Responses ◽  
Ascochyta Rabiei ◽  
Ros Production ◽  
Gene Encoding ◽  
Adaptation Mechanism ◽  
Basal Resistance ◽  
Cell Turgor ◽  
Strong Candidate

Drought and leaf blight caused by the fungus Ascochyta rabiei often co-occur in chickpea (Cicer arietinum)-producing areas. While the responses of chickpea to either drought or A. rabiei infection have been extensively studied, their combined effect on plant defense mechanisms is unknown. Fine modulation of stress-induced signaling pathways under combined stress is an important stress adaptation mechanism that warrants a better understanding. Here we show that drought facilitates resistance against A. rabiei infection in chickpea. The analysis of proline levels and gene expression profiling of its biosynthetic pathway under combined drought and A. rabiei infection revealed the gene encoding proline dehydrogenase (CaProDH2) as a strong candidate conferring resistance to A. rabiei infection. Transcript levels of CaProDH2, pyrroline-5-carboxylate (P5C) quantification, and measurement of mitochondrial reactive oxygen species (ROS) production showed that fine modulation of the proline-P5C cycle determines the observed resistance. In addition, CaProDH2-silenced plants lost basal resistance to A. rabiei infection induced by drought, while overexpression of the gene conferred higher resistance to the fungus. We suggest that the drought-induced accumulation of proline in the cytosol helps maintain cell turgor and raises mitochondrial P5C contents by a CaProDH2-mediated step, which results in ROS production that boosts plant defense responses and confers resistance to A. rabiei infection. Our findings indicate that manipulating the proline-P5C pathway may be a possible strategy for improving stress tolerance in plants suffering from combined drought and A. rabiei infection.

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