Histopathology reveals correlative and unique phenotypes in a high-throughput mouse phenotyping screen

The Mouse Genetics Project (MGP) at the Wellcome Trust Sanger Institute aims to generate and phenotype over 800 genetically modified mouse lines over the next 5 years to gain a better understanding of mammalian gene function and provide an invaluable resource to the scientific community for follow-up studies. Phenotyping includes the generation of a standardized biobank of paraffin-embedded tissues for each mouse line, but histopathology is not routinely performed. In collaboration with the Pathology Core of the Centre for Modeling Human Disease (CMHD) we report the utility of histopathology in a high-throughput primary phenotyping screen. Histopathology was assessed in an unbiased selection of 50 mouse lines with (n=30) or without (n=20) clinical phenotypes detected by the standard MGP primary phenotyping screen. Our findings revealed that histopathology added correlating morphological data in 19 of 30 lines (63.3%) in which the primary screen detected a phenotype. In addition, seven of the 50 lines (14%) presented significant histopathology findings that were not associated with or predicted by the standard primary screen. Three of these seven lines had no clinical phenotype detected by the standard primary screen. Incidental and strain-associated background lesions were present in all mutant lines with good concordance to wild-type controls. These findings demonstrate the complementary and unique contribution of histopathology to high-throughput primary phenotyping of mutant mice.KEY WORDS: Histopathology, High-throughput phenotyping, Mouse, Pathology     

Trade-offs between tRNA abundance and mRNA secondary structure support smoothing of translation elongation rate

Translation of protein from mRNA is a complex multi-step process that occurs at a non-uniform rate. Variability in ribosome speed along an mRNA enables refinement of the proteome and plays a critical role in protein biogenesis. Detailed single protein studies have found both tRNA abundance and mRNA secondary structure as key modulators of translation elongation rate, but recent genome-wide ribosome profiling experiments have not observed significant influence of either on translation efficiency. Here we provide evidence that this results from an inherent trade-off between these factors. We find codons pairing to high-abundance tRNAs are preferentially used in regions of high secondary structure content, while codons read by significantly less abundant tRNAs are located in lowly structured regions. By considering long stretches of high and low mRNA secondary structure in Saccharomyces cerevisiae and Escherichia coli and comparing them to randomized-gene models and experimental expression data, we were able to distinguish clear selective pressures and increased protein expression for specific codon choices. The trade-off between secondary structure and tRNA-concentration based codon choice allows for compensation of their independent effects on translation, helping to smooth overall translational speed and reducing the chance of potentially detrimental points of excessively slow or fast ribosome movement.     

Suppression of recJ mutations of Escherichia coli by mutations in translation initiation factor IF3.

We have isolated genetic suppressors of mutations in the recJ gene of Escherichia coli in a locus we term srjA. These srjA mutations cause partial to complete alleviation of the recombination and UV repair defects conferred by recJ153 and recJ154 mutations in a recBC sbcA genetic background. The srjA gene was mapped to 37.5 min on the E. coli chromosome. This chromosomal region from the srjA5 strain was cloned into a plasmid vector and was shown to confer recJ suppression in a dominant fashion. Mutational analysis of this plasmid mapped srjA to the infC gene encoding translation initiation factor 3 (IF3). Sequence analysis revealed that all three srjA alleles cause amino acid substitutions of IF3. Suppression of recJ was shown to be allele specific: recJ153 and recJ154 mutations were suppressible, but recJ77 and the insertion allele recJ284::Tn10 were not. In addition, growth medium-conditional lethality was observed for strains carrying srjA mutations with the nonsuppressible recJ alleles. When introduced into recJ+ strains, srjA mutations conferred hyperrecombinational and hyper-UVr phenotypes. An interesting implication of these genetic properties of srjA suppression is that IF3 may regulate the expression of recJ and perhaps other recombination genes and hence may regulate the recombinational capacity of the cell.     

Suppression of temperature-sensitive sporulation of a Bacillus subtilis elongation factor G mutant by RNA polymerase mutations.

A class of rifampin-resistant (rfm) mutations of Bacillus subtilis suppresses the temperature-sensitive sporulation of a fusidic acid-resistant mutant. FUS426, which has an altered elongation factor G. The rfm mutation suppressed only the sporulation defect caused by the elongation factor G mutation, but could not suppress other types of induced sporulation defects. Genetic and biochemical analyses showed that the sporulation suppression by the rfm mutation was caused by a single mutation in RNA polymerase. After the early sporulation phase, the apparent rate of RNA synthesis of FUS426, measured by [3H]uracil or [3H]uridine incorporation into RNA, became lower than that of the wild-type strain, and this decrease was reversed by the rfm mutation. However, when the total rate of RNA synthesis of FUS426 was calculated by measuring the specific activity of [3H]UTP and [3H]CTP, it was higher than that of the rfm mutant, RIF122FUS426. The possible mechanism of the functional interaction between elongation factor G and RNA polymerase during sporulation is discussed.     

Influence of the growth rate calculation on the relationship between growth rate and temperature

Three calculations of the growth rate (e.g. slope of a plot of the log10 of cfu ml-1 vs time, mum of the Gompertz equation and the reciprocal of time to obtain 108 cfu ml-1) were compared for Escherichia coli TG1 growing in tryptone soy broth medium at temperatures ranging from 14 to 39 degrees C. Up to now, the influence of using such different definitions on the relationship between microbial growth rate and temperature has never been investigated. In order to compare these calculation procedures, a dimensionless analysis based on the following normalized variables, mudim = mu/muopt and Tdim = [T-Tmin]/[Topt-Tmin], was used (Dantigny 1998). The influence of suboptimal temperatures on the growth rate was represented by means of a Belehràdek-type model based on a power function law: [mudim] = [Tdim]alpha. The influence of the different growth rate calculations on the model constants was assessed. Despite the great dependence of the raw growth rate values on the calculation procedure, the dimensionless analysis demonstrated that the alpha-value is independent of the growth rate definition. This result suggests that any definition for the growth rate can be utilized in studies aimed at determining the influence of temperature on microbial growth and highlights the interest of using dimensionless variables to overcome differences in the order of magnitude of the growth rate data and to avoid confusion between definitions.     

Competition between trans-translation and termination or elongation of translation

The effects of tRNA, RF1 and RRF on trans-translation by tmRNA were examined using a stalled complex of ribosome prepared using a synthetic mRNA and pure Escherichia coli translation factors. No endoribonucleolytic cleavage of mRNA around the A site was found in the stalled ribosome and was required for the tmRNA action. When the A site was occupied by a stop codon, alanyl-tmRNA competed with RF1 with the efficiency of peptidyl-transfer to alanyl-tmRNA for trans-translation inversely correlated to the efficiency of translation termination. The competition was not affected by RF3. A sense codon also serves as a target for alanyl-tmRNA with competition of aminoacyl-tRNA. The extent of inhibition was decreased with the length of the 3′-extension of mRNA. RRF, only at a high concentration, slightly affected peptidyl-transfer for trans-translation, although it did not affect the canonical elongation. These results indicate that alanyl-tmRNA does not absolutely require the truncation of mRNA around the A site but prefers an mRNA of a short 3′-extension from the A site and that it can operate on either a sense or termination codon at the A site, at which alanyl-tmRNA competes with aminoacyl-tRNA, RF and RRF.     

Dominant-negative mutant phenotypes and the regulation of translation elongation factor 2 levels in yeast

The eukaryotic translation elongation factor 2 (eEF2), a member of the G-protein superfamily, catalyzes the post-peptidyl transferase translocation of deacylated tRNA and peptidyl tRNA to the ribosomal E- and P-sites. eEF2 is modified by a unique post-translational modification: the conversion of His699 to diphthamide at the tip of domain IV, the region proposed to mimic the anticodon of tRNA. Structural models indicate a hinge is important for conformational changes in eEF2. Mutations of V488 in the hinge region and H699 in the tip of domain IV produce non-functional mutants that when co-expressed with the wild-type eEF2 result in a dominant-negative growth phenotype in the yeast Saccharomyces cerevisiae. This phenotype is linked to reduced levels of the wild-type protein, as total eEF2 levels are unchanged. Changes in the promoter, 5′-untranslated region (5′-UTR) or 3′-UTR of the EFT2 gene encoding eEF2 do not allow overexpression of the protein, showing that eEF2 levels are tightly regulated. The H699K mutant, however, also alters translation phenotypes. The observed regulation suggests that the cell needs an optimum amount of active eEF2 to grow properly. This provides information about a new mechanism by which translation is efficiently maintained.     

Suppression of defective-sporulation phenotypes by mutations in transcription factor genes of Bacillus subtilis.

Mutations in the Bacillus subtilis major RNA polymerase sigma factor gene (rpoD/crsA47) and a sensory receiver gene (spoOA/rvtA11) are potent intergenic suppressors of several stage 0 sporulation mutations (spoOB, OE, OF & OK). We show here that these suppressors also rescue temperature-sensitive sporulation phenotypes (Spots) caused by mutations in RNA polymerase, ribosomal protein, and protein synthesis elongation factor EF-G genes. The effects of the crsA and rvtA suppressors on RNA polymerase and ribosomal protein spots mutations are similar to those previously described for mutations in another intergenic suppressor gene rev. We have examined the effects of rvtA and crsA mutations on the expression of sporulation-associated membrane proteins, including flagellin and penicillin binding protein 5* (PBP 5*). Both suppressors restored sporulation and synthesis of PBP 5* in several spoO mutants. However, only rvtA restored flagellin synthesis in spoO suppressed backgrounds. The membrane protein phenotypes resulting from the presence of crsA or rvtA suppressors in spoO strains suggests that these suppressors function via distinct molecular mechanisms. The rvtA and crsA mutations are also able to block the ability of ethanol to induce spoO phenocopies at concentrations of ethanol which prevent sporulation in wild type cells. The effects of ethanol on sporulation-associated membrane protein synthesis in wild type and suppressor containing strains have been examined.     

COMP mutations: domain-dependent relationship between abnormal chondrocyte trafficking and clinical PSACH and MED phenotypes

Mutations in cartilage oligomeric matrix protein (COMP) produce clinical phenotypes ranging from the severe end of the spectrum, pseudoachondroplasia (PSACH), which is a dwarfing condition, to a mild condition, multiple epiphyseal dysplasia (MED). Patient chondrocytes have a unique morphology characterized by distended rER cisternae containing lamellar deposits of COMP and other extracellular matrix proteins. It has been difficult to determine why different mutations give rise to variable clinical phenotypes. Using our in vitro cell system, we previously demonstrated that the most common PSACH mutation, D469del, severely impedes trafficking of COMP and type IX collagen in chondrocytic cells, consistent with observations from patient cells. Here, we hypothesize that PSACH and MED mutations variably affect the cellular trafficking behavior of COMP and that the extent of defective trafficking correlates with clinical phenotype. Twelve different recombinant COMP mutations were expressed in rat chondrosarcoma cells and the percent cells with ER-retained COMP was assessed. For mutations in type 3 (T3) repeats, trafficking defects correlated with clinical phenotype; PSACH mutations had more cells retaining mutant COMP, while MED mutations had fewer. In contrast, the cellular trafficking pattern observed for mutations in the C-terminal globular domain (CTD) was not predictive of clinical phenotype. The results demonstrate that different COMP mutations in the T3 repeat domain have variable effects on intracellular transport, which correlate with clinical severity, while CTD mutations do not show such a correlation. These findings suggest that other unidentified factors contribute to the effect of the CTD mutations. J. Cell. Biochem. 103: 778-787, 2008. (c) 2007 Wiley-Liss, Inc.     

Growth and translation elongation rate are sensitive to the concentration of EF-Tu

We have used quantitative immunoblotting to estimate the amount of EF-Tu in a variety of S. typhimurium strains with wild-type, mutant, insertionally inactivated or plasmid-borne tuf genes. In the same strains we have measured translation elongation rate, exponential growth rate and the level of nonsense codon readthrough. In the wild-type strain, at moderate to fast growth rates, our data show that EF-Tu makes up 8–9% of total cell protein. Strains with either of the tuf genes insertionally inactivated have 65% of the wild-type EF-Tu level, irrespective of which tuf gene remains active, or whether that gene is wild-type or a kirromycin-resistant mutant. Strains with only one active tuf gene have reduced growth and translation elongation rates. From the magnitude of the reduction in elongation rate relative to the level of EF-Tu we calculate that in glucose minimal medium the in vivo saturation level of wild-type ribosomes by ternary complexes is only 63%. Strains with a ribosome mutation causing a poor interaction with ternary complex are non-viable on minimal medium when the level of EF-Tu is reduced.     

The relationship between leaf growth and ABA accumulation in the grass leaf elongation zone

Detached barley (Hordeum vulgare L.) shoots, maintained at different air temperatures and VPDs, were fed ABA via the sub-crown internode in a leaf elongation assay. Analysis of variance of leaf elongation rate (LER) showed significant effects of temperature (T), fed [ABA] and the interaction T × [ABA]. However, the interaction became non-significant when LER was modelled against the [ABA] of the elongation zone, [EZ-ABA] When detached barley shoots were fed sap from droughted maize (Zea mays L.) plants, sap [ABA] could not explain the growth inhibitory activity. Measurement of [EZ-ABA] accounted for this ‘unexplained’ growth inhibition. The detached shoot experiments indicated that [EZ-ABA], and not xylem sap [ABA], was an appropriate explanatory variable to measure in droughted plants. However, ABA accumulation in the elongation zone could not explain a 35% growth reduction in intact droughted plants; thus we considered an interaction of water status and ABA. Using a coleoptile growth assay, we applied mild osmotic stresses (ψ=0 to ?0.06 MPa) and 10^?4 mol m^?3 ABA. Individually, these treatments did not inhibit growth. However, osmotic stress and ABA applied together significantly reduced growth. This interaction may be an important mechanism in explaining leaf growth inhibition of droughted plants.     

Relationship between root elongation rate and diameter and duration of growth of lateral roots of maize

The objective of this work was to describe the relationship between elongation rate and diameter of maize roots and to estimate the length and growth duration of lateral roots of maize. Diameters and elongation rates of roots were measuredin situ on plants grown 5 weeks in small rhizotrons under greenhouse conditions. At the end of the experimental period the roots were harvested and diameters of axile and lateral roots were measured. The frequency distribution of diameters of harvested roots was bimodal with a minimum at 0.6 mm; 97% of axile roots were larger than this value and 98% of the lateral roots were smaller. Root elongation per day increased as diameter increased but the slope of the relationship with lateral roots was about 2.5 times that with axile roots when separate linear regressions were fitted to the two populations. The length of lateral roots found on axillary roots between the base and about 30 cm from the apex was approximately 2.2 cm. All of the data was consistent with the hypothesis that the lateral roots grew for about 2.5 days and then ceased growing. The axillary roots continued to grow throughout the experimental period at a rate of about 3 cm day⁻¹. Contribution from the Department of Agronomy, New York State College of Agriculture and Life Sciences, Cornell University, Ithaca, NY 14853. Agronomy paper No. 1661. This research is part of the program of the Center for Root-Soil Research.     

The relationship between nutrient feed rate and specific growth rate in fed batch cultures

Summary Equations are described which relate nutrient feed rate to specific microbial growth rate in fed batch culture. Fed batch cultures are classified into three types: 1) those allowing constant specific microbial growth rate, 2) those in which the rate of change of flow rate is constant and 3) those in which the nutrient flow rate is constant. The basic properties of these three types are described.Symbols F medium flow rate, L³ T^–1 - F _o medium flow rate at zero time, L³ T^–1 - g rate of change of flow rate with time, L³ T^–2 - K _v volume constant, being the total cell weight at zero time divided by the product of the yield coefficient and growth-limiting substrate concentration in the feed, L³ - s _r growth limiting substrate concentration in the feed, ML^–3 - V volume of liquid in the growth vessel, L³ - V _f volume of medium fed to the growth vessel, L³ - V _o volume of liquid in the growth vessel at zero time, L³ - X total weight of cells, M - x concentration of cells, ML^–3 - X _g total weight of cells grown, M - X _o total weight of cells at zero time, M - Y yield coefficient, weight of cells grown per unit weight of growth-limiting substrate - specific microbial growth rate, T^–1