Mutagenesis of the L, M, and N subunits of Complex I from Escherichia coli indicates a common role in function

Background

The membrane arm of Complex I (NADH:ubiquinone oxidoreductase) contains three large, and closely related subunits, which are called L, M, and N in E. coli. These subunits are homologous to components of multi-subunit Na⁺/H⁺ antiporters, and so are implicated in proton translocation.

Methodology/Principal Findings

Nineteen site-specific mutations were constructed at two corresponding positions in each of the three subunits. Two positions were selected in each subunit: L_K169, M_K173, N_K158 and L_Q236, M_H241, N_H224. Membrane vesicles were prepared from all of the resulting mutant strains, and were assayed for deamino-NADH oxidase activity, proton translocation, ferricyanide reductase activity, and sensitivity to capsaicin. Corresponding mutations in the three subunits were found to have very similar effects on all activities measured. In addition, the effect of adding exogenous decylubiquinone on these activities was tested. 50 µM decylubiquinone stimulated both deamino-NADH oxidase activity and proton translocation by wild type membrane vesicles, but was inhibitory towards the same activities by membrane vesicles bearing the lysine substitution at the L236/M241/N224 positions.

Conclusions/Significance

The results show a close correlation with reduced activity among the corresponding mutations, and provide evidence that the L, M, and N subunits have a common role in Complex I.     

Mutational Analysis of Highly Conserved Residues in the Phage PhiC31 Integrase Reveals Key Amino Acids Necessary for the DNA Recombination

Background

Amino acid sequence alignment of phage phiC31 integrase with the serine recombinases family revealed highly conserved regions outside the catalytic domain. Until now, no system mutational or biochemical studies have been carried out to assess the roles of these conserved residues in the recombinaton of phiC31 integrase.

Methodology/Principal Findings

To determine the functional roles of these conserved residues, a series of conserved residues were targeted by site-directed mutagenesis. Out of the 17 mutants, 11 mutants showed impaired or no recombination ability, as analyzed by recombination assay both in vivo and in vitro. Results of DNA binding activity assays showed that mutants (R18A, I141A, L143A,E153A, I432A and V571A) exhibited a great decrease in DNA binding affinity, and mutants (G182A/F183A, C374A, C376A/G377A, Y393A and V566A) had completely lost their ability to bind to the specific target DNA attB as compared with wild-type protein. Further analysis of mutants (R18A, I141A, L143A and E153A) synapse and cleavage showed that these mutants were blocked in recombination at the stage of strand cleavage.

Conclusions/Significance

This data reveals that some of the highly conserved residues both in the N-terminus and C-terminus region of phiC31 integrase, play vital roles in the substrate binding and cleavage. The cysteine-rich motif and the C-tail val-rich region of phiC31 integrase may represent the major DNA binding domains of phiC31 integrase.     

Histidine hydrogen-deuterium exchange mass spectrometry for probing the microenvironment of histidine residues in dihydrofolate reductase

Background

Histidine Hydrogen-Deuterium Exchange Mass Spectrometry (His-HDX-MS) determines the HDX rates at the imidazole C₂-hydrogen of histidine residues. This method provides not only the HDX rates but also the pK _a values of histidine imidazole rings. His-HDX-MS was used to probe the microenvironment of histidine residues of E. coli dihydrofolate reductase (DHFR), an enzyme proposed to undergo multiple conformational changes during catalysis.

Methodology/Principal Findings

Using His-HDX-MS, the pK _a values and the half-lives (t _1/2) of HDX reactions of five histidine residues of apo-DHFR, DHFR in complex with methotrexate (DHFR-MTX), DHFR in complex with MTX and NADPH (DHFR-MTX-NADPH), and DHFR in complex with folate and NADP⁺ (DHFR-folate-NADP⁺) were determined. The results showed that the two parameters (pK _a and t _1/2) are sensitive to the changes of the microenvironment around the histidine residues. Although four of the five histidine residues are located far from the active site, ligand binding affected their pK _a, t _1/2 or both. This is consistent with previous observations of ligand binding-induced distal conformational changes on DHFR. Most of the observed pK _a and t _1/2 changes could be rationalized using the X-ray structures of apo-DHFR, DHFR-MTX-NADPH, and DHFR-folate-NADP⁺. The availability of the neutron diffraction structure of DHFR-MTX enabled us to compare the protonation states of histidine imidazole rings.

Conclusions/Significance

Our results demonstrate the usefulness of His-HDX-MS in probing the microenvironments of histidine residues within proteins.     

A comprehensive evaluation of potential lung function associated genes in the SpiroMeta general population sample

Rationale

Lung function measures are heritable traits that predict population morbidity and mortality and are essential for the diagnosis of chronic obstructive pulmonary disease (COPD). Variations in many genes have been reported to affect these traits, but attempts at replication have provided conflicting results. Recently, we undertook a meta-analysis of Genome Wide Association Study (GWAS) results for lung function measures in 20,288 individuals from the general population (the SpiroMeta consortium).

Objectives

To comprehensively analyse previously reported genetic associations with lung function measures, and to investigate whether single nucleotide polymorphisms (SNPs) in these genomic regions are associated with lung function in a large population sample.

Methods

We analysed association for SNPs tagging 130 genes and 48 intergenic regions (+/−10 kb), after conducting a systematic review of the literature in the PubMed database for genetic association studies reporting lung function associations.

Results

The analysis included 16,936 genotyped and imputed SNPs. No loci showed overall significant association for FEV₁ or FEV₁/FVC traits using a carefully defined significance threshold of 1.3×10⁻⁵. The most significant loci associated with FEV₁ include SNPs tagging MACROD2 (P = 6.81×10⁻⁵), CNTN5 (P = 4.37×10⁻⁴), and TRPV4 (P = 1.58×10⁻³). Among ever-smokers, SERPINA1 showed the most significant association with FEV₁ (P = 8.41×10⁻⁵), followed by PDE4D (P = 1.22×10⁻⁴). The strongest association with FEV₁/FVC ratio was observed with ABCC1 (P = 4.38×10⁻⁴), and ESR1 (P = 5.42×10⁻⁴) among ever-smokers.

Conclusions

Polymorphisms spanning previously associated lung function genes did not show strong evidence for association with lung function measures in the SpiroMeta consortium population. Common SERPINA1 polymorphisms may affect FEV₁ among smokers in the general population.     

Differential inhibitory effects of CysLT(1) receptor antagonists on P2Y(6) receptor-mediated signaling and ion transport in human bronchial epithelia

Background

Cysteinyl leukotriene (CysLT) is one of the proinflammatory mediators released by the bronchi during inflammation. CysLTs exert their biological effects via specific G-protein-coupled receptors. CysLT₁ receptor antagonists are available for clinical use for the treatment of asthma. Recently, crosstalk between CysLT₁ and P2Y₆ receptors has been delineated. P2Y receptors are expressed in apical and/or basolateral membranes of virtually all polarized epithelia to control the transport of fluid and electrolytes. Previous research suggests that CysLT₁ receptor antagonists inhibit the effects of nucleotides acting at P2Y receptors. However, the detailed molecular mechanism underlying the inhibition remains unresolved.

Methodology/Principal Findings

In this study, western blot analysis confirmed that both CysLT₁ and P2Y₆ receptors were expressed in the human bronchial epithelial cell line 16HBE14o-. All three CysLT₁ antagonists inhibited the uridine diphosphate (UDP)-evoked I_SC, but only montelukast inhibited the UDP-evoked [Ca²⁺]_i increase. In the presence of forskolin or 8-bromoadenosine 3′5′ cyclic monophosphate (8-Br-cAMP), the UDP-induced I_SC was potentiated but was reduced by pranlukast and zafirlukast but not montelukast. Pranlukast inhibited the UDP-evoked I_SC potentiated by an Epac activator, 8-(4-Chlorophenylthio)-2′-O-methyladenosine-3′,5′-cyclic monophosphate (8-CPT-2′-O-Me-cAMP), while montelukast and zafirlukast had no such effect. Pranlukast inhibited the real-time increase in cAMP changes activated by 8-CPT-2′-O-Me-cAMP as monitored by fluorescence resonance energy transfer imaging. Zafirlukast inhibited the UDP-induced I_SC potentiated by N⁶- Phenyladenosine- 3′, 5′- cyclic monophosphorothioate, Sp- isomer (Sp-6-Phe-cAMP; a PKA activator) and UDP-activated PKA activity.

Conclusions/Significance

In summary, our data strongly suggest for the first time that in human airway epithelia, the three specific CysLT₁ receptor antagonists exert differential inhibitory effects on P2Y₆ receptor-coupled Ca²⁺ signaling pathways and the potentiating effect on I_SC mediated by cAMP and Epac, leading to the modulation of ion transport activities across the epithelia.     

Variance of the SGK1 gene is associated with insulin secretion in different European populations: results from the TUEF, EUGENE2, and METSIM studies

Hypothesis

Serum- and Glucocorticoid-inducible Kinase 1 (SGK1) is involved in the regulation of insulin secretion and may represent a candidate gene for the development of type 2 diabetes mellitus in humans.

Methods

Three independent European populations were analyzed for the association of SGK1 gene (SGK) variations and insulin secretion traits. The German TUEF project provided the screening population (N = 725), and four tagging SNPs (rs1763527, rs1743966, rs1057293, rs9402571) were investigated. EUGENE2 (N = 827) served as a replication cohort for the detected associations. Finally, the detected associations were validated in the METSIM study, providing 3798 non-diabetic and 659 diabetic (type 2) individuals.

Results

Carriers of the minor G allele in rs9402571 had significantly higher C-peptide levels in the 2 h OGTT (+10.8%, p = 0.04; dominant model) and higher AUC_C-Peptide/AUC_Glc ratios (+7.5%, p = 0.04) compared to homozygous wild type TT carriers in the screening population. As interaction analysis for BMI×rs9402571 was significant (p = 0.04) for the endpoint insulin secretion, we stratified the TUEF cohort for BMI, using a cut off point of BMI = 25. The effect on insulin secretion only remained significant in lean TUEF participants (BMI≤25). This finding was replicated in lean EUGENE2 rs9402571 minor allele carriers, who had a significantly higher AUC_Ins/AUC_Glc (TT: 226±7, XG: 246±9; p = 0.019). Accordingly, the METSIM trial revealed a lower prevalence of type 2 diabetes (OR: 0.85; 95%CI: 0.71–1.01; p = 0.065, dominant model) in rs9402571 minor allele carriers.

Conclusions

The rs9402571 SGK genotype associates with increased insulin secretion in lean non-diabetic TUEF/EUGENE2 participants and with lower diabetes prevalence in METSIM. Our study in three independent European populations supports the conclusion that SGK variability affects diabetes risk.     

Phosphorylation-dependent protein interaction with Trypanosoma brucei 14-3-3 proteins that display atypical target recognition

Background

The 14-3-3 proteins are structurally conserved throughout eukaryotes and participate in protein kinase signaling. All 14-3-3 proteins are known to bind to evolutionally conserved phosphoserine-containing motifs (modes 1 and/or 2) with high affinity. In Trypanosoma brucei, 14-3-3I and II play pivotal roles in motility, cytokinesis and the cell cycle. However, none of the T. brucei 14-3-3 binding proteins have previously been documented.

Methodology/Principal Findings

Initially we showed that T. brucei 14-3-3 proteins exhibit far lower affinity to those peptides containing RSxpSxP (mode 1) and RxY/FxpSxP (mode 2) (where x is any amino acid residue and pS is phosphoserine) than human 14-3-3 proteins, demonstrating the atypical target recognition by T. brucei 14-3-3 proteins. We found that the putative T. brucei protein phosphatase 2C (PP2c) binds to T. brucei 14-3-3 proteins utilizing its mode 3 motif (–pS/pTx_1-2-COOH, where x is not Pro). We constructed eight chimeric PP2c proteins replacing its authentic mode 3 motif with potential mode 3 sequences found in Trypanosoma brucei genome database, and tested their binding. As a result, T. brucei 14-3-3 proteins interacted with three out of eight chimeric proteins including two with high affinity. Importantly, T. brucei 14-3-3 proteins co-immunoprecipitated with an uncharacterized full-length protein containing identified high-affinity mode 3 motif, suggesting that both proteins form a complex in vivo. In addition, a synthetic peptide derived from this mode 3 motif binds to T. brucei 14-3-3 proteins with high affinity.

Conclusion/Significance

Because of the atypical target recognition of T. brucei 14-3-3 proteins, no 14-3-3-binding proteins have been successfully identified in T. brucei until now whereas over 200 human 14-3-3-binding proteins have been identified. This report describes the first discovery of the T. brucei 14-3-3-binding proteins and their binding motifs. The high-affinity phosphopeptide will be a powerful tool to identify novel T. brucei 14-3-3-binding proteins.     

Amino acids involved in polyphosphate synthesis and its mobilization are distinct in polyphosphate kinase-1 from Mycobacterium tuberculosis

Background

In bacteria polyphosphates (poly-P) are involved in cellular metabolism and development especially during stress. The enzyme, principally involved in polyphosphate biosynthesis and its mobilization leading to generation of NTPs, is known as polyphosphate kinase (PPK).

Principal Findings

Among two genes of polyphosphate kinases present in Mycobacterium tuberculosis, we cloned and expressed PPK1 in Escherichia coli as histidine-tagged protein. This ∼86 kDa protein is capable of autophosphorylation and synthesis of poly-P as well as NTP. Among 22 conserved histidine residues, we found only His-491 is autophosphorylated and crucial for any enzymatic activity. Substitution of His-510 caused mPPK1 protein deficient but not defective in autophosphorylation, thereby contrary to earlier reports negating any role of this residue in the process. However, mutation of His-510 with either Ala or Gln affected ATP or poly-P synthesis depending on the substitution; while such effects were severe with H510A but mild with H510Q. Furthermore, mPPK1 also renders auxiliary nucleotide diphosphate kinase function by synthesizing virtually all NTPs/dNTPs from their cognate NDPs/dNDPs by utilizing poly-P as the phosphate donor albeit with varied efficiency. To assess the influence of other catalytic domain residues of mPPK1 towards its functionality, we designed mutations based on E. coli PPK1 crystal structure since it owes 68% amino acid sequence similarity with mPPK1. Interestingly, our results revealed that mutations in mPPK1 affecting poly-P synthesis always affected its ATP synthesizing ability; however, the reverse may not be true.

Conclusions/Significance

We conclude that amino acid residues involved in poly-P and ATP synthesizing activities of mPPK1 are distinct. Considering conserved nature of PPK1, it seems our observations have broader implications and not solely restricted to M. tuberculosis only.     

Dichogamy correlates with outcrossing rate and defines the selfing syndrome in the mixed-mating genus Collinsia

Background and Aims

How and why plants evolve to become selfing is a long-standing evolutionary puzzle. The transition from outcrossing to highly selfing is less well understood in self-compatible (SC) mixed-mating (MM) species where potentially subtle interactions between floral phenotypes and the environment are at play. We examined floral morphological and developmental traits across an entire SC MM genus, Collinsia, to determine which, if any, predict potential autonomous selfing ability when pollinators are absent (AS) and actual selfing rates in the wild, s_m, and to best define the selfing syndrome for this clade.

Methods

Using polymorphic microsatellite markers, we obtained 30 population-level estimates of s_m across 19 Collinsia taxa. Species grand means for the timing of herkogamy (stigma–anther contact) and dichogamy (stigmatic receptivity, SR), AS, floral size, longevity and their genetic correlations were quantified for 22 taxa.

Key Results

Species fell into discrete selfing and outcrossing groups based on floral traits. Loss of dichogamy defines Collinsia''s selfing syndrome. Floral size, longevity and herkogamy also differ significantly between these groups. Most taxa have high AS rates (>80 %), but AS is uncorrelated with any measured trait. In contrast, s_m is significantly correlated only with SR. High variance in s_m was observed in the two groups.

Conclusions

Collinsia species exhibit clear morphological and developmental traits diagnostic of ‘selfing’ or ‘outcrossing’ groups. However, many species in both the ‘selfing’ and the ‘outcrossing’ groups were MM, pointing to the critical influence of the pollination environment, the timing of AS and outcross pollen prepotency on s_m. Flower size is a poor predictor of Collinsia species'' field selfing rates and this result may apply to many SC species. Assessment of the variation in the pollination environment, which can increase selfing rates in more ‘outcrossing’ species but can also decrease selfing rates in more ‘selfing’ species, is critical to understanding mating system evolution of SC MM taxa.     

Simulating the influence of vernalization, photoperiod and optimum temperature on wheat developmental rates

Background and Aims

Accurately representing development is essential for applying crop simulations to investigate the effects of climate, genotypes or crop management. Development in wheat (Triticum aestivum, T. durum) is primarily driven by temperature, but affected by vernalization and photoperiod, and is often simulated by reducing thermal-time accumulation using vernalization or photoperiod factors or limiting accumulation when a lower optimum temperature (T_optl) is exceeded. In this study T_optl and methods for representing effects of vernalization and photoperiod on anthesis were examined using a range of planting dates and genotypes.

Methods

An examination was made of T_optl values of 15, 20, 25 and 50 °C, and either the most limiting or the multiplicative value of the vernalization and photoperiod development rate factors for simulating anthesis. Field data were from replicated trials at Ludhiana, Punjab, India with July through to December planting dates and seven cultivars varying in vernalization response.

Key Results

Simulations of anthesis were similar for T_optl values of 20, 25 and 50 °C, but a T_optl of 15 °C resulted in a consistent bias towards predicting anthesis late for early planting dates. Results for T_optl above 15 °C may have occurred because mean temperatures rarely exceeded 20 °C before anthesis for many planting dates. For cultivars having a strong vernalization response, anthesis was more accurately simulated when vernalization and photoperiod factors were multiplied rather than using the most limiting of the two factors.

Conclusions

Setting T_optl to a high value (30 °C) and multiplying the vernalization and photoperiod factors resulted in accurately simulating anthesis for a wide range of planting dates and genotypes. However, for environments where average temperatures exceed 20 °C for much of the pre-anthesis period, a lower T_optl (23 °C) might be appropriate. These results highlight the value of testing a model over a wide range of environments.Key words: Wheat, Triticum aestivum, T. durum, air temperature, thermal time, shoot apex, phenology, growth stages, anthesis, flowering     

Recovery dynamics of growth, photosynthesis and carbohydrate accumulation after de-submergence: a comparison between two wetland plants showing escape and quiescence strategies

Background and Aims

The capacity for fast-growth recovery after de-submergence is important for establishment of riparian species in a water-level-fluctuation zone. Recovery patterns of two wetland plants, Alternanthera philoxeroides and Hemarthria altissima, showing ‘escape’ and ‘quiescence’ responses, respectively, during submergence were investigated.

Methods

Leaf and root growth and photosynthesis were monitored continuously during 10 d of recovery following 20 d of complete submergence. Above- and below-ground dry weights, as well as carbohydrate concentrations, were measured several times during the experiment.

Key Results

Both species remobilized stored carbohydrate during submergence. Although enhanced internode elongation depleted the carbohydrate storage in A. philoxeroides during submergence, this species resumed leaf growth 3 d after de-submergence concomitant with restoration of the maximal photosynthetic capacity. In contrast, some sucrose was conserved in shoots of H. altissima during submergence, which promoted rapid re-growth of leaves 2 d after de-submergence and earlier than the full recovery of photosynthesis. The recovery of root growth was delayed by 1–2 d compared with leaves in both species.

Conclusions

Submergence tolerance of the escape and quiescence strategies entails not only the corresponding regulation of growth, carbohydrate catabolism and energy metabolism during submergence but also co-ordinated recovery of photosynthesis, growth and carbohydrate partitioning following de-submergence.     

Temporal trends in the impact factor of European versus USA biomedical journals

Background

The impact factors of biomedical journals tend to rise over time. We sought to assess the trend in the impact factor, during the past decade, of journals published on behalf of United States (US) and European scientific societies, in four select biomedical subject categories (Biology, Cell Biology, Critical Care Medicine, and Infectious Diseases).

Methods

We identified all journals included in the above-mentioned subject categories of Thomson Reuters Journal Citation Reports® for the years 1999, 2002, 2005, and 2008. We selected those that were published on behalf of US or European scientific societies, as documented in journal websites.

Results

We included 167 journals (35 in the subject category of Biology, 79 in Cell Biology, 27 in Critical Care Medicine, and 26 in Infectious Diseases). Between 1999 and 2008, the percentage increase in the impact factor of the European journals was higher than for the US journals (73.7±110.0% compared with 39.7±70.0%, p = 0.049). Regarding specific subject categories, the percentage change in the factor of the European journals tended to be higher than the respective US journals for Cell Biology (61.7% versus 16.3%), Critical Care Medicine (212.4% versus 65.4%), Infectious Diseases (88.3% versus 48.7%), whereas the opposite was observed for journals in Biology (41.0% versus 62.5%).

Conclusion

Journals published on behalf of European scientific societies, in select biomedical fields, may tend to close the “gap” in impact factor compared with those of US societies.

What''s Already Known About This Topic?

The impact factors of biomedical journals tend to rise through years. The leading positions in productivity in biomedical research are held by developed countries, including those from North America and Western Europe.

What Does This Article Add?

The journals from European biomedical scientific societies tended, over the past decade, to increase their impact factor more than the respective US journals.     

Assessing the role of CD103 in immunity to an intestinal helminth parasite

Background

In the intestine, the integrin CD103 is expressed on a subset of T regulatory (T_reg) cells and a population of dendritic cells (DCs) that produce retinoic acid and promote immune homeostasis. However, the role of CD103 during intestinal helminth infection has not been tested.

Methodology/Principal Findings

We demonstrate that CD103 is dispensable for the development of protective immunity to the helminth parasite Trichuris muris. While we observed an increase in the frequency of CD103⁺ DCs in the lamina propria (LP) following acute high-dose infection with Trichuris, lack of CD103 had no effect on the frequency of CD11c⁺ DCs in the LP or mesenteric lymph nodes (mLN). CD103-deficient (CD103^−/−) mice develop a slightly increased and earlier T cell response but resolve infection with similar kinetics to control mice. Similarly, low-dose chronic infection of CD103^−/− mice with Trichuris resulted in no significant difference in immunity or parasite burden. Absence of CD103 also had no effect on the frequency of CD4⁺CD25⁺Foxp3⁺ T_reg cells in the mLN or LP.

Conclusions/Significance

These results suggest that CD103 is dispensable for intestinal immunity during helminth infection. Furthermore, lack of CD103 had no effect on DC or T_reg recruitment or retention within the large intestine.     

Asthma prevalence associated with geographical latitude and regional insolation in the United States of America and Australia

Background

It has been proposed that vitamin D deficiency may be responsible for an increase in the prevalence of allergic diseases and asthma worldwide. Human ability to generate physiologically required quantities of vitamin D through sun exposure is decreasing with increasing geographical latitude.

Objectives

Considering that vitamin D deficiency is usually due to lack of outdoor sun exposure, this study is designed to test the hypothesis that a higher prevalence of asthma should be expected at high relative to low geographical latitudes.

Methods

Linear regression analyses are performed on asthma prevalence in the U.S. adult population vs. geographical latitude, insolation, air temperature, and air pollution (PM_2.5) for 97 major metropolitan/micropolitan statistical areas of the continental United States of America and on general population asthma prevalence vs. geographical latitude in eight metropolitan areas of Australia.

Results

A 10° change in geographical latitude from southern to northern regions of the Eastern Seaboard is associated with a 2% increase in adult asthma prevalence (p<0.001). Total insolation in winter months is almost as strong as latitude in its ability to explain the observed spatial variation in the prevalence of asthma (r² = 0.43; p<0.001). Similar results are obtained using the Australian data (r² = 0.73; p<0.01), suggesting a consistent association between the latitude/insolation and asthma prevalence worldwide.

Conclusions

The results of this study suggest that, as a known modulator of the immune response closely linked with the geographical latitude and erythemal UV irradiation, vitamin D may play an important role in the development/exacerbation of asthma.     

Biochemical and molecular characterization of the gentisate transporter GenK in Corynebacterium glutamicum

Background

Gentisate (2,5-dihydroxybenzoate) is a key ring-cleavage substrate involved in various aromatic compounds degradation. Corynebacterium glutamicum ATCC13032 is capable of growing on gentisate and genK was proposed to encode a transporter involved in this utilization by its disruption in the restriction-deficient mutant RES167. Its biochemical characterization by uptake assay using [¹⁴C]-labeled gentisate has not been previously reported.

Methodology/Principal Findings

In this study, biochemical characterization of GenK by uptake assays with [¹⁴C]-labeled substrates demonstrated that it specifically transported gentisate into the cells with V _max and K_m of 3.06±0.16 nmol/min/mg of dry weight and 10.71±0.11 µM respectively, and no activity was detected for either benzoate or 3-hydoxybenzoate. When GenK was absent in strain RES167 ΔgenK, it retained 85% of its original transport activity at pH 6.5 compared to that of strain RES167. However, it lost 79% and 88% activity at pH 7.5 and 8.0, respectively. A number of competing substrates, including 3-hydroxybenzoate, benzoate, protocatechuate and catechol, significantly inhibited gentisate uptake by more than 40%. Through site-directed mutagenesis, eight amino acid residues of GenK, Asp-54, Asp-57 and Arg-386 in the hydrophobic transmembrane regions and Arg-103, Trp-309, Asp-312, Arg-313 and Ile-317 in the hydrophilic cytoplasmic loops were shown to be important for gentisate transport. When conserved residues Asp-54 and Asp-57 respectively were changed to glutamate, both mutants retained approximately 50% activity and were able to partially complement the ability of strain RES167 ΔgenK to grow on gentisate.

Conclusions/Significance

Our results demonstrate that GenK is an active gentisate transporter in Corynebacterium glutamicum ATCC13032. The GenK-mediated gentisate transport was also shown to be a limiting step for the gentisate utilization by this strain. This enhances our understanding of gentisate transport in the microbial degradation of aromatic compounds.     

Crystal structures of archaemetzincin reveal a moldable substrate-binding site

Background

Archaemetzincins are metalloproteases occurring in archaea and some mammalia. They are distinct from all the other metzincins by their extended active site consensus sequence HEXXHXXGXXHCX₄CXMX₁₇CXXC featuring four conserved cysteine residues. Very little is known about their biological importance and structure-function relationships.

Principal Findings

Here we present three crystal structures of the archaemetzincin AfAmzA (Uniprot {"type":"entrez-protein","attrs":{"text":"O29917","term_id":"74514303","term_text":"O29917"}}O29917) from Archaeoglobus fulgidus, revealing a metzincin architecture featuring a zinc finger-like structural element involving the conserved cysteines of the consensus motif. The active sites in all three structures are occluded to different extents rendering the enzymes proteolytically inactive against a large variety of tested substrates. Owing to the different ligand binding there are significant differences in active site architecture, revealing a large flexibility of the loops covering the active site cleft.

Conclusions

The crystal structures of AfAmzA provide the structural basis for the lack of activity in standard proteolytic assays and imply a triggered activity onset upon opening of the active site cleft.