Using stable MutS dimers and tetramers to quantitatively analyze DNA mismatch recognition and sliding clamp formation

The process of DNA mismatch repair is initiated when MutS recognizes mismatched DNA bases and starts the repair cascade. The Escherichia coli MutS protein exists in an equilibrium between dimers and tetramers, which has compromised biophysical analysis. To uncouple these states, we have generated stable dimers and tetramers, respectively. These proteins allowed kinetic analysis of DNA recognition and structural analysis of the full-length protein by X-ray crystallography and small angle X-ray scattering. Our structural data reveal that the tetramerization domains are flexible with respect to the body of the protein, resulting in mostly extended structures. Tetrameric MutS has a slow dissociation from DNA, which can be due to occasional bending over and binding DNA in its two binding sites. In contrast, the dimer dissociation is faster, primarily dependent on a combination of the type of mismatch and the flanking sequence. In the presence of ATP, we could distinguish two kinetic groups: DNA sequences where MutS forms sliding clamps and those where sliding clamps are not formed efficiently. Interestingly, this inability to undergo a conformational change rather than mismatch affinity is correlated with mismatch repair.     

ScrG, a GGDEF-EAL protein, participates in regulating swarming and sticking in Vibrio parahaemolyticus

In this work, we describe a new gene controlling lateral flagellar gene expression. The gene encodes ScrG, a protein containing GGDEF and EAL domains. This is the second GGDEF-EAL-encoding locus determined to be involved in the regulation of swarming: the first was previously characterized and named scrABC (for "swarming and capsular polysaccharide regulation"). GGDEF and EAL domain-containing proteins participate in the synthesis and degradation of the nucleotide signal cyclic di-GMP (c-di-GMP) in many bacteria. Overexpression of scrG was sufficient to induce lateral flagellar gene expression in liquid, decrease biofilm formation, decrease cps gene expression, and suppress the DeltascrABC phenotype. Removal of its EAL domain reversed ScrG activity, converting ScrG to an inhibitor of swarming and activator of cps expression. Overexpression of scrG decreased the intensity of a (32)P-labeled nucleotide spot comigrating with c-di-GMP standard, whereas overexpression of scrG(Delta)(EAL) enhanced the intensity of the spot. Mutants with defects in scrG showed altered swarming and lateral flagellin production and colony morphology (but not swimming motility); furthermore, mutation of two GGDEF-EAL-encoding loci (scrG and scrABC) produced cumulative effects on swarming, lateral flagellar gene expression, lateral flagellin production and colony morphology. Mutant analysis supports the assignment of the primary in vivo activity of ScrG to acting as a phosphodiesterase. The data are consistent with a model in which multiple GGDEF-EAL proteins can influence the cellular nucleotide pool: a low concentration of c-di-GMP favors surface mobility, whereas high levels of this nucleotide promote a more adhesive Vibrio parahaemolyticus cell type.     

Slow base excision by human alkyladenine DNA glycosylase limits the rate of formation of AP sites and AP endonuclease 1 does not stimulate base excision

The base excision repair pathway removes damaged DNA bases and resynthesizes DNA to replace the damage. Human alkyladenine DNA glycosylase (AAG) is one of several damage-specific DNA glycosylases that recognizes and excises damaged DNA bases. AAG removes primarily damaged adenine residues. Human AP endonuclease 1 (APE1) recognizes AP sites produced by DNA glycosylases and incises the phophodiester bond 5' to the damaged site. The repair process is completed by a DNA polymerase and DNA ligase. If not tightly coordinated, base excision repair could generate intermediates that are more deleterious to the cell than the initial DNA damage. The kinetics of AAG-catalyzed excision of two damaged bases, hypoxanthine and 1,N6-ethenoadenine, were measured in the presence and absence of APE1 to investigate the mechanism by which the base excision activity of AAG is coordinated with the AP incision activity of APE1. 1,N6-ethenoadenine is excised significantly slower than hypoxanthine and the rate of excision is not affected by APE1. The excision of hypoxanthine is inhibited to a small degree by accumulated product, and APE1 stimulates multiple turnovers by alleviating product inhibition. These results show that APE1 does not significantly affect the kinetics of base excision by AAG. It is likely that slow excision by AAG limits the rate of AP site formation in vivo such that AP sites are not created faster than can be processed by APE1.     

Distinct effects of atypical 1,4-dihydropyridines on 1-methyl-4-phenylpyridinium-induced toxicity

Our previous data obtained from in vivo experiments demonstrated high neuroprotective effects of three novel atypical neuronal non-calcium antagonistic 1,4-dihydropyridine (DHP) derivatives cerebrocrast, glutapyrone and tauropyrone. The present studies were carried out in vitro to clarify, at least in part, their mechanism of action in primary culture of cerebellar granule cells by use of 1-methyl-4-phenylpyridinium (MPP+) as a neurotoxic agent which causes dramatic oxidative stress. Cerebrocrast (highly lipophilic, with a classical two-ring structure) dose-dependently (0.01-10.0 microM, EC50 = 13 nM) reduced MPP+-induced cell death. At the same time, the calcium antagonist nimodipine (reference drug) protected cell death at much higher concentrations (EC50 = 12.4 microM). Cerebrocrast decreased also the generation of reactive oxygen species and loss of mitochondrial membrane potential. In contrast, low lipophilic amino acid-containing DHPs glutapyrone and tauropyrone (glutamate- and taurine-containing, correspondingly) were without significant effects indicating their distinct mode of action in comparison to cerebrocrast. We have demonstrated for the first time an ability of atypical non-calcium antagonistic DHP cerebrocrast (which has classical DHP structure elements and high lipophilicity) to protect MPP+-induced deterioration of mitochondrial bioenergetics. One may suggest mitochondria as an essential intracellular target for the neuroprotective action of cerebrocrast and indicate its usefulness in the treatment of Parkinson's disease.     

Anciently duplicated <Emphasis Type="Italic">Broad Complex</Emphasis> exons have distinct temporal functions during tissue morphogenesis

Broad Complex (BRC) is an essential ecdysone-pathway gene required for entry into and progression through metamorphosis in Drosophila melanogaster. Mutations of three BRC complementation groups cause numerous phenotypes, including a common suite of morphogenesis defects involving central nervous system (CNS), adult salivary glands (aSG), and male genitalia. These defects are phenocopied by the juvenile hormone mimic methoprene. Four BRC isoforms are produced by alternative splicing of a protein-binding BTB/POZ-encoding exon (BTB _BRC ) to one of four tandemly duplicated, DNA-binding zinc-finger-encoding exons (Z1 _BRC , Z2 _BRC , Z3 _BRC , Z4 _BRC ). Highly conserved orthologs of BTB _BRC and all four Z _BRC were found among published cDNA sequences or genome databases from Diptera, Lepidoptera, Hymenoptera, and Coleoptera, indicating that BRC arose and underwent internal exon duplication before the split of holometabolous orders. Tramtrack subfamily members, abrupt, tramtrack, fruitless, longitudinals lacking (lola), and CG31666 were characterized throughout Holometabola and used to root phylogenetic analyses of Z _BRC exons, which revealed that the Z _BRC clade includes Z _abrupt . All four Z _BRC domains, including Z4 _BRC , which has no known essential function, are evolving in a manner consistent with selective constraint. We used transgenic rescue to explore how different BRC isoforms contribute to shared tissue-morphogenesis functions. As predicted from earlier studies, the common CNS and aSG phenotypes were rescued by BRC-Z1 in rbp mutants, BRC-Z2 in br mutants, and BRC-Z3 in 2Bc mutants. However, the isoforms are required at two different developmental stages, with BRC-Z2 and -Z3 required earlier than BRC-Z1. The sequential action of BRC isoforms indicates subfunctionalization of duplicated Z _BRC exons even when they contribute to common developmental processes. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Activity of the RhoU/Wrch1 GTPase is critical for cranial neural crest cell migration

The neural crest (NC) is a stem cell-like population that arises at the border of neural and non-neural ectoderm. During development, NC undergoes an epithelio-mesenchymal transition (EMT), i.e. loss of epithelial junctions and acquisition of pro-migratory properties, invades the entire embryo and differentiates into a wide diversity of terminal tissues. We have studied the implication of Rho pathways in NC development and previously showed that RhoV is required for cranial neural crest (CNC) cell specification. We show here that the non-canonical Wnt response rhoU/wrch1 gene, closely related to rhoV, is also expressed in CNC cells but at later stages. Using both gain- and loss-of-function experiments, we demonstrate that the level of RhoU expression is critical for CNC cell migration and subsequent differentiation into craniofacial cartilages. In in vitro cultures, RhoU activates pathways that cooperate with PAK1 and Rac1 in epithelial adhesion, cell spreading and directional cell migration. These data support the conclusion that RhoU is an essential regulator of CNC cell migration.     

Neighbourhood analysis as an indicator of spatial requirements of broiler chickens

The appropriate stocking density for broiler chickens is a much discussed topic in animal welfare. To determine at which stocking density the level of crowding becomes aversive to 4–6-week-old broiler chickens, spatial distribution and behaviour of groups stocked at 8, 19, 29, 40, 45, 51, 61 or 72 birds per 3.3 m² were analysed. Spatial distribution was evaluated using three different indices: inter-individual distances, nearest neighbour distances and Dirichlet polygon areas. The assumption was that broilers would increase the distance to their pen mates if high densities (i.e., close proximity to pen mates) were experienced as aversive, whereas they would decrease this distance if close proximity was experienced positively. Increased distances to pen mates would lead to increased nearest neighbour distances and a more homogeneous distribution (i.e., lower variation of inter-individual distances and of Dirichlet-polygon size) than expected by chance. The distribution expected by chance was determined from both a random distribution and a ‘resource-corrected’ random distribution (which incorporated environmental influences on spatial distribution but excluded social ones).Behavioural observations showed that at higher stocking densities more sitting bouts (P = 0.003) and adjustments of the sitting and lying posture (P < 0.001) occurred. It was also found that nearest neighbour distance varied according to behaviour (P = 0.001). Birds that were eating/drinking were further apart from their nearest neighbour than birds that were foraging, preening, adjusting their sitting or lying posture or showing “other” behaviour.The results from all three methods of spatial analysis suggested that broilers in groups ≥19 birds per 3.3 m² (ultimately equivalent to 15 kg/m²) started to experience the proximity of conspecifics as aversive at some point during the last 3 weeks of rearing. However, nearest neighbour distance analysis showed evidence of aversiveness earlier in life than the other methods of analyzing spatial distribution (variation in inter-individual distance and polygon size), suggesting that nearest neighbour distance is the more sensitive indicator of space requirements.When uneven use of the different areas within the pen was reflected in the expected distribution (i.e., for comparisons to the resource-corrected random distribution) different results were obtained than when such measures were omitted (i.e., for comparisons to the random distribution). As such, this study emphasises the importance of accounting for environmental influences on distribution within a pen.     

Taxonomy of Marine Bacteria: Beneckea parahaemolytica and Beneckea alginolytica

A collection of 169 strains, including 91 obtained from cases of gastroenteritis and 41 from localized tissue infections and infections of the eye and ear, was submitted to an extensive nutritional, physiological, and morphological characterization. The nutritional and physiological data obtained from these strains, as well as data for strains of other species of the genus Beneckea, were submitted to a numerical analysis which grouped the strains into clusters on the basis of phenotypic similarity. Strains from cases of gastroenteritis formed a group of three clusters which linked at a similarity value of 68%. These three clusters could not, however, be separated from each other by universally positive or negative traits, and on the basis of their overall phenotypic similarity were assigned to a single species, B. parahaemolytica. The majority of the strains from human, nonenteric sources segregated into two distinct clusters, one designated B. alginolytica and the other unassigned with respect to species (group C-2). B. parahaemolytica, B. alginolytica, and group C-2 could be readily distinguished from one another as well as from the remaining species of the genus Beneckea by multiple, unrelated, phenotypic traits. Activities of selected enzymes of glucose and gluconate catabolism in cell-free extracts of B. parahaemolytica, B. alginolytica, and group C-2 suggested that these organisms utilized glucose primarily via the Embden-Meyerhof pathway and gluconate primarily via the Entner-Doudoroff pathway. Similar results were observed in the other members of the genus Beneckea.