scholarly journals Essential Bacterial Functions Encoded by Gene Pairs

2006 ◽  
Vol 189 (2) ◽  
pp. 591-602 ◽  
Author(s):  
Helena B. Thomaides ◽  
Ella J. Davison ◽  
Lisa Burston ◽  
Hazel Johnson ◽  
David R. Brown ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Gene Duplication ◽  
Minimal Medium ◽  
Single Gene ◽  
Species Conservation ◽  
The Other ◽  
Bacterial Genomes ◽  
Putative Protein ◽  
Gene Pairs ◽  
New Genes

ABSTRACT To address the need for new antibacterials, a number of bacterial genomes have been systematically disrupted to identify essential genes. Such programs have focused on the disruption of single genes and may have missed functions encoded by gene pairs or multiple genes. In this work, we hypothesized that we could predict the identity of pairs of proteins within one organism that have the same function. We identified 135 putative protein pairs in Bacillus subtilis and attempted to disrupt the genes forming these, singly and then in pairs. The single gene disruptions revealed new genes that could not be disrupted individually and other genes required for growth in minimal medium or for sporulation. The pairwise disruptions revealed seven pairs of proteins that are likely to have the same function, as the presence of one protein can compensate for the absence of the other. Six of these pairs are essential for bacterial viability and in four cases show a pattern of species conservation appropriate for potential antibacterial development. This work highlights the importance of combinatorial studies in understanding gene duplication and identifying functional redundancy.

scholarly journals Tetracycline Induces Stabilization of mRNA in Bacillus subtilis

2002 ◽  
Vol 184 (4) ◽  
pp. 889-894 ◽  
Author(s):  
Yi Wei ◽  
David H. Bechhofer
Keyword(s):  
Bacillus Subtilis ◽  
Mrna Stability ◽  
The Other ◽  
Leader Region ◽  
Subinhibitory Concentration ◽  
Coding Sequence ◽  
Mrna Stabilization ◽  
Threefold Increase ◽  
The Stability

ABSTRACT The tet(L) gene of Bacillus subtilis confers low-level tetracycline (Tc) resistance. Previous work examining the >20-fold-inducible expression of tet(L) by Tc demonstrated a 12-fold translational induction. Here we show that the other component of tet(L) induction is at the level of mRNA stabilization. Addition of a subinhibitory concentration of Tc results in a two- to threefold increase in tet(L) mRNA stability. Using a plasmid-borne derivative of tet(L) with a large in-frame deletion of the coding sequence, the mechanism of Tc-induced stability was explored by measuring the decay of tet(L) mRNAs carrying specific mutations in the leader region. The results of these experiments, as well as experiments with a B. subtilis strain that is resistant to Tc due to a mutation in the ribosomal S10 protein, suggest different mechanisms for the effects of Tc on translation and on mRNA stability. The key role of the 5" end in determining mRNA stability was confirmed in these experiments. Surprisingly, the stability of several other B. subtilis mRNAs was also induced by Tc, which indicates that addition of Tc may result in a general stabilization of mRNA.

scholarly journals Whole-Genome Analysis of Genes Regulated by the Bacillus subtilis Competence Transcription Factor ComK

2002 ◽  
Vol 184 (9) ◽  
pp. 2344-2351 ◽  
Author(s):  
Mitsuo Ogura ◽  
Hirotake Yamaguchi ◽  
Kazuo Kobayashi ◽  
Naotake Ogasawara ◽  
Yasutaro Fujita ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Bacillus Subtilis ◽  
Genetic Transformation ◽  
Dna Microarray ◽  
Genome Analysis ◽  
Transformation Efficiency ◽  
The Other ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Microarray Technique

ABSTRACT The Bacillus subtilis competence transcription factor ComK is required for establishment of competence for genetic transformation. In an attempt to study the ComK factor further, we explored the genes regulated by ComK using the DNA microarray technique. In addition to the genes known to be dependent on ComK for expression, we found many genes or operons whose ComK dependence was not known previously. Among these genes, we confirmed the ComK dependence of 16 genes by using lacZ fusions, and three genes were partially dependent on ComK. Transformation efficiency was significantly reduced in an smf disruption mutant, although disruption of the other ComK-dependent genes did not result in significant decreases in transformation efficiency. Nucleotide sequences similar to that of the ComK box were found for most of the newly discovered genes regulated by ComK.

scholarly journals Inheritance Patterns of Coat Colouration and Horn Number in Jacob Sheep

2018 ◽  
Vol 3 (1) ◽  
pp. 363-367
Author(s):  
N.R. McEwan ◽  
O.A. Anjola
Keyword(s):  
Gene Locus ◽  
Single Gene ◽  
Coat Colour ◽  
The Body ◽  
The Other ◽  
Limiting Factors ◽  
Inheritance Patterns ◽  
Mode Of Inheritance

Abstract The allele for black coat colour is dominant relative to the allele for lilac in Jacob sheep and is affected by a single gene locus. The percentage of this colouration, as opposed to white fleece, across the body has a heritability value of 0.255. The mode of inheritance for horn number in these animals is less clear, with neither the trait for 2 horns, nor for 4 horns being totally dominant, based on crosses of 2 x 2-horned parents and 4 x 4-horned parents; although in these examples the majority of lambs had the same number of horns as their parents. However, when one parent had 2 horns and the other had 4 horns, the gender of the 4-horned parent appeared to influence the frequency of 4-horned offspring; 77% of lambs born to a 4-horned dam being 4-horned, but only 50% when the 4-horned parent was the sire. These data suggest evidence for sex-limiting factors being involved in determining the number of horns in this breed.

Dynamic localization of penicillin-binding proteins during spore development in Bacillus subtilis

Microbiology ◽  
2005 ◽  
Vol 151 (3) ◽  
pp. 999-1012 ◽  
Author(s):  
Dirk-Jan Scheffers
Keyword(s):  
Bacillus Subtilis ◽  
Green Fluorescent Protein ◽  
Binding Proteins ◽  
Cytoplasmic Membrane ◽  
Fluorescent Protein ◽  
Spore Formation ◽  
The Other ◽  
Spore Development ◽  
Penicillin Binding Proteins ◽  
Green Fluorescent

During Bacillus subtilis spore formation, many membrane proteins that function in spore development localize to the prespore septum and, subsequently, to the outer prespore membrane. Recently, it was shown that the cell-division-specific penicillin-binding proteins (PBPs) 1 and 2b localize to the asymmetric prespore septum. Here, the author studied the localization of other PBPs, fused to green fluorescent protein (GFP), during spore formation. Fusions to PBPs 4, 2c, 2d, 2a, 3, H, 4b, 5, 4a, 4* and X were expressed during vegetative growth, and their localization was monitored during sporulation. Of these PBPs, 2c, 2d, 4b and 4* have been implicated as having a function in sporulation. It was found that PBP2c, 2d and X changed their localization, while the other PBPs tested were not affected. The putative endopeptidase PbpX appears to spiral out in a pattern that resembles FtsZ redistribution during sporulation, but a pbpX knockout strain had no distinguishable phenotype. PBP2c and 2d localize to the prespore septum and follow the membrane during engulfment, and so are redistributed to the prespore membrane. A similar pattern was observed when GFP–PBP2c was expressed in the mother cell from a sporulation-specific promoter. This work shows that various PBPs known to function during sporulation are redistributed from the cytoplasmic membrane to the prespore.

IX.—The Intellectual Resemblance of Twins

1934 ◽  
Vol 53 ◽  
pp. 105-129 ◽  
Author(s):  
Louis Herrman ◽  
Lancelot Hogben
Keyword(s):  
Physical Environment ◽  
Social Behaviour ◽  
Narrow Range ◽  
Single Gene ◽  
Experimental Methods ◽  
The Other ◽  
Genetic Constitution ◽  
Family Influences ◽  
Social And Physical Environment ◽  
The One

The characteristics of social behaviour in man are conditioned by previous experience. What is observed is the product on the one hand of a certain genetic constitution and on the other of an intricate, prolonged, and at present largely obscure, process of training and physical environment, including both the environment of the fœtus and family influences, social and physical. The experimental methods for detecting differences due to single gene substitutions cannot be applied directly. Indeed, we can see no immediate prospect of applying to social behaviour methods of genetic analysis such as have led to the mapping of the chromosomes in animals and in plants. With methods available at present, genetic inquiry can undertake to detect whether any gene differences are associated with observed differences, and whether such gene differences are recognisable throughout a comparatively wide or narrow range of social and physical environment.

scholarly journals Toxin–Antitoxin Systems in Bacillus subtilis

Toxins ◽  
2019 ◽  
Vol 11 (5) ◽  
pp. 262 ◽  
Author(s):  
Sabine Brantl ◽  
Peter Müller
Keyword(s):  
Bacillus Subtilis ◽  
Physiological Role ◽  
Present Knowledge ◽  
The Other ◽  
Type I ◽  
Type Ii ◽  
Free Living ◽  
Bacterial Chromosomes ◽  
Maintenance Systems ◽  
Living Bacteria

Toxin–antitoxin (TA) systems were originally discovered as plasmid maintenance systems in a multitude of free-living bacteria, but were afterwards found to also be widespread in bacterial chromosomes. TA loci comprise two genes, one coding for a stable toxin whose overexpression kills the cell or causes growth stasis, and the other coding for an unstable antitoxin that counteracts toxin action. Of the currently known six types of TA systems, in Bacillus subtilis, so far only type I and type II TA systems were found, all encoded on the chromosome. Here, we review our present knowledge of these systems, the mechanisms of antitoxin and toxin action, and the regulation of their expression, and we discuss their evolution and possible physiological role.

scholarly journals Comparisons of Visual Rust Assessments and DNA Levels of Phakopsora pachyrhizi in Soybean Genotypes Varying in Rust Resistance

Plant Disease ◽  
2011 ◽  
Vol 95 (8) ◽  
pp. 1007-1012 ◽  
Author(s):  
C. Paul ◽  
C. B. Hill ◽  
G. L. Hartman
Keyword(s):  
Quantitative Polymerase Chain Reaction ◽  
Single Gene ◽  
The Other ◽  
Soybean Rust ◽  
Disease Assessment ◽  
Fungal Colonization ◽  
Phakopsora Pachyrhizi ◽  
Breeding Populations ◽  
Soybean Genotypes ◽  
Infection Types

Soybean resistance to Phakopsora pachyrhizi, the cause of soybean rust, has been characterized by the following three infection types: (i) immune response (IM; complete resistance) with no visible lesions, (ii) resistant reaction with reddish brown (RB) lesions (incomplete resistance), and (iii) susceptible reaction with tan-colored (TAN) lesions. Based on visual assessments of these phenotypes, single gene resistance in soybean to P. pachyrhizi has been documented, but colonization within infected tissues based on fungal DNA (FDNA) levels in different soybean genotypes had not been analyzed. The research used a quantitative polymerase chain reaction (Q-PCR) assay to compare visual disease assessment to FDNA in controlled inoculation experiments using two isolates of P. pachyrhizi. The objective of the first experiment was to compare data from digital visual disease assessment to FDNA from Q-PCR assays using digital visual disease assessment using five resistant soybean genotypes (one IM and four RB) and five susceptible genotypes (TAN). The objective of the second experiment was to quantify FDNA using Q-PCR at different time points after inoculation to determine if levels of fungal colonization differed in five soybean genotypes with different levels of resistance (one IM, two RB, and two TAN). For experiment 1, the numbers of uredinia and uredinia per lesion on four of the five resistant soybean genotypes were lower (P < 0.05) than the other six genotypes. Significant differences (P < 0.05) in FDNA concentrations were found among soybean genotypes with TAN lesions and among soybean genotypes with RB lesions. Soybean cultivar UG5 (IM phenotype) had significantly less (P < 0.05) FDNA than all of the other genotypes. Some genotypes that produced TAN lesions had significantly lower (P < 0.05) or non-significantly different FDNA concentrations compared to those genotypes that produced RB lesions. For experiment 2, the regression of FDNA on days after inoculation was significant (P < 0.01) with positive slopes for all genotypes except for UG5, in which FDNA declined over time, indicating a reduction of fungal colonization. The results of this Q-PCR FDNA screening technique demonstrates its use to distinguish different types of resistance, and could be used to facilitate the evaluation of soybean breeding populations, where precise quantification of incomplete and/or partial resistance is needed to identify and map quantitative trait loci.

scholarly journals Sporulation in Bacillus subtilis. Correlation of biochemical events with morphological changes in asporogeneous mutants

1970 ◽  
Vol 118 (4) ◽  
pp. 667-676 ◽  
Author(s):  
W. M. Waites ◽  
D. Kay ◽  
I. W. Dawes ◽  
D. A. Wood ◽  
S. C. Warren ◽  
...  
Keyword(s):  
Alkaline Phosphatase ◽  
Bacillus Subtilis ◽  
Cell Division ◽  
Biochemical Marker ◽  
Morphological Changes ◽  
Glucose Dehydrogenase ◽  
Stage Iv ◽  
The Other ◽  
Stage Ii ◽  
Stage Iii

A comparison was made of morphological changes and successive, mainly biochemical, marker events for sporulation in 14 asporogenous mutants. The morphological and biochemical sequences are linked so that arrested development in one is accompanied by corresponding effects in the other. Thus mutants that fail to produce both protease and antibiotic do not progress beyond stage 0, formation of alkaline phosphatase appears to be associated with the transition from stage II to stage III and glucose dehydrogenase with that from stage III to stage IV. Stage II mutants may produce `pygmy' cells or other bizarre cell-division forms. The biochemical sequence is dependent in the sense that if the occurrence of any one event is blocked that of all the succeeding events is also blocked. This has implications for biochemical models that have been proposed to explain the temporal sequence observed in spore development.

scholarly journals Contributions of Rare Gene Variants to Familial and Sporadic FSGS

2019 ◽  
Vol 30 (9) ◽  
pp. 1625-1640 ◽  
Author(s):  
Minxian Wang ◽  
Justin Chun ◽  
Giulio Genovese ◽  
Andrea U. Knob ◽  
Ava Benjamin ◽  
...  
Keyword(s):  
Rare Variants ◽  
Single Gene ◽  
Genetic Diagnosis ◽  
Unrelated Family ◽  
The Past ◽  
New Genes ◽  
Rare Gene ◽  
Gene Defects ◽  
Disease Associated Genes ◽  
Burden Tests

BackgroundOver the past two decades, the importance of genetic factors in the development of FSGS has become increasingly clear. However, despite many known monogenic causes of FSGS, single gene defects explain only 30% of cases.MethodsTo investigate mutations underlying FSGS, we sequenced 662 whole exomes from individuals with sporadic or familial FSGS. After quality control, we analyzed the exome data from 363 unrelated family units with sporadic or familial FSGS and compared this to data from 363 ancestry-matched controls. We used rare variant burden tests to evaluate known disease-associated genes and potential new genes.ResultsWe validated several FSGS-associated genes that show a marked enrichment of deleterious rare variants among the cases. However, for some genes previously reported as FSGS related, we identified rare variants at similar or higher frequencies in controls. After excluding such genes, 122 of 363 cases (33.6%) had rare variants in known disease-associated genes, but 30 of 363 controls (8.3%) also harbored rare variants that would be classified as “causal” if detected in cases; applying American College of Medical Genetics filtering guidelines (to reduce the rate of false-positive claims that a variant is disease related) yielded rates of 24.2% in cases and 5.5% in controls. Highly ranked new genes include SCAF1, SETD2, and LY9. Network analysis showed that top-ranked new genes were located closer than a random set of genes to known FSGS genes.ConclusionsAlthough our analysis validated many known FSGS-causing genes, we detected a nontrivial number of purported “disease-causing” variants in controls, implying that filtering is inadequate to allow clinical diagnosis and decision making. Genetic diagnosis in patients with FSGS is complicated by the nontrivial rate of variants in known FSGS genes among people without kidney disease.

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