TAT-Pathway-Dependent Lipoproteins as a Niche-Based Adaptation in Prokaryotes

Bacterial lipoproteins, characterized by the N-terminal N-acyl S-diacylglyceryl Cysteine, are key membrane proteins in bacterial homeostasis. It is generally thought that during the modification lipoprotein precursors are translocated via the Sec-machinery in an unfolded state. The recent discovery of twin-arginine translocation (TAT) machinery, meant for exporting folded-proteins, and the presence of TAT-type signal sequences in co-factor-containing (hence already folded) lipoproteins, prompted us to investigate its role and significance in lipoprotein biosynthesis. We systematically analyzed 696 prokaryotic genomes using an algorithm based on DOLOP and TatP rules to predict TAT-pathway-dependent lipoprotein substrates. Occurrence of the deduced TAT-pathway-dependent lipoprotein substrates in relation to genome size, presence or absence of TAT machinery, and extent of its usage for lipoprotein export and habitat types revealed that unlike the host-obligates, the free-living prokaryotes in complex hostile environments (e.g., soil) depend more on TAT-exported lipoproteins. Functional classification of the predicted TAT-dependent lipoproteins revealed enrichment in hydrolases and oxido-reductases, which are fast-folding and co-factor-containing proteins. The role of the TAT pathway in the export of folded-lipoproteins and in niche-specific adaptation for survival has important implications not only in lipoprotein biosynthesis, but also for protein and metabolic engineering applications.     

Genome Reduction Promotes Increase in Protein Functional Complexity in Bacteria

Obligate pathogenic and endosymbiotic bacteria typically experience gene loss due to functional redundancy, asexuality, and genetic drift. We hypothesize that reduced genomes increase their functional complexity through protein multitasking, in which many genes adopt new roles to counteract gene loss. Comparisons of interaction networks among six bacteria that have varied genome sizes (Mycoplasma pneumoniae, Treponema pallidum, Helicobacter pylori, Campylobacter jejuni, Synechocystis sp., and Mycobacterium tuberculosis) reveal that proteins in small genomes interact with proteins from a wider range of functions than do their orthologs in larger genomes. This suggests that surviving proteins form increasingly complex functional relationships to compensate for genes that are lost.     

Environmental Pressure May Change the Composition Protein Disorder in Prokaryotes

Many prokaryotic organisms have adapted to incredibly extreme habitats. The genomes of such extremophiles differ from their non-extremophile relatives. For example, some proteins in thermophiles sustain high temperatures by being more compact than homologs in non-extremophiles. Conversely, some proteins have increased volumes to compensate for freezing effects in psychrophiles that survive in the cold. Here, we revealed that some differences in organisms surviving in extreme habitats correlate with a simple single feature, namely the fraction of proteins predicted to have long disordered regions. We predicted disorder with different methods for 46 completely sequenced organisms from diverse habitats and found a correlation between protein disorder and the extremity of the environment. More specifically, the overall percentage of proteins with long disordered regions tended to be more similar between organisms of similar habitats than between organisms of similar taxonomy. For example, predictions tended to detect substantially more proteins with long disordered regions in prokaryotic halophiles (survive high salt) than in their taxonomic neighbors. Another peculiar environment is that of high radiation survived, e.g. by Deinococcus radiodurans. The relatively high fraction of disorder predicted in this extremophile might provide a shield against mutations. Although our analysis fails to establish causation, the observed correlation between such a simplistic, coarse-grained, microscopic molecular feature (disorder content) and a macroscopic variable (habitat) remains stunning.     

Functional and Structural Diversity of Insect Glutathione S-transferases in Xenobiotic Adaptation

As a superfamily of multifunctional enzymes that is mainly associated with xenobiotic adaptation, glutathione S-transferases (GSTs) facilitate insects'' survival under chemical stresses in their environment. GSTs confer xenobiotic adaptation through direct metabolism or sequestration of xenobiotics, and/or indirectly by providing protection against oxidative stress induced by xenobiotic exposure. In this article, a comprehensive overview of current understanding on the versatile functions of insect GSTs in detoxifying chemical compounds is presented. The diverse structures of different classes of insect GSTs, specifically the spatial localization and composition of their amino acid residues constituted in their active sites are also summarized. Recent availability of whole genome sequences of numerous insect species, accompanied by RNA interference, X-ray crystallography, enzyme kinetics and site-directed mutagenesis techniques have significantly enhanced our understanding of functional and structural diversity of insect GSTs.     

Imaging Functional and Structural Brain Connectomics in Attention-Deficit/Hyperactivity Disorder

Attention-deficit/hyperactivity disorder (ADHD) is one of the most common neurodevelopment disorders in childhood. Clinically, the core symptoms of this disorder include inattention, hyperactivity, and impulsivity. Previous studies have documented that these behavior deficits in ADHD children are associated with not only regional brain abnormalities but also changes in functional and structural connectivity among regions. In the past several years, our understanding of how ADHD affects the brain’s connectivity has been greatly advanced by mapping topological alterations of large-scale brain networks (i.e., connectomes) using noninvasive neurophysiological and neuroimaging techniques (e.g., electroencephalograph, functional MRI, and diffusion MRI) in combination with graph theoretical approaches. In this review, we summarize the recent progresses of functional and structural brain connectomics in ADHD, focusing on graphic analysis of large-scale brain systems. Convergent evidence suggests that children with ADHD had abnormal small-world properties in both functional and structural brain networks characterized by higher local clustering and lower global integrity, suggesting a disorder-related shift of network topology toward regular configurations. Moreover, ADHD children showed the redistribution of regional nodes and connectivity involving the default-mode, attention, and sensorimotor systems. Importantly, these ADHD-associated alterations significantly correlated with behavior disturbances (e.g., inattention and hyperactivity/impulsivity symptoms) and exhibited differential patterns between clinical subtypes. Together, these connectome-based studies highlight brain network dysfunction in ADHD, thus opening up a new window into our understanding of the pathophysiological mechanisms of this disorder. These works might also have important implications on the development of imaging-based biomarkers for clinical diagnosis and treatment evaluation in ADHD.     

Cold Adaptation: Structural and Functional Characterizations of Psychrophilic and Mesophilic Acetate Kinase

Acetate kinase catalyzes the reversible magnesium-dependent phosphoryl transfer from ATP to acetate to form acetyl phosphate and ADP. Here, we report functional and some structural properties of cold-adapted psychrotrophic enzyme; acetate kinase with those from mesophilic counterpart in Escherichia coli K-12. Recombinant acetate kinase from Shewanella sp. AS-11 (SAK) and E. coli K-12 (EAK) were purified to homogeneity following affinity chromatography and followed by Super Q column chromatography as reported before [44]. Both purified enzymes are shared some of the common properties such as (similar molecular mass, amino acid sequence and similar optimum pH), but characterized shift in the apparent optimum temperature of specific activity to lower temperature as well as by a lower thermal stability compared with EAK. The functional comparisons reveal that SAK is a cold adapted enzyme, having a higher affinity to acetate than EAK. In the acetyl phosphate and ADP-forming direction, the catalytic efficiency (k _cat/K _m) for acetate was 8.0 times higher for SAK than EAK at 10 °C. The activity ratio of SAK to EAK was increased with decreasing temperature in both of the forward and backward reactions. Furthermore, the activation energy, enthalpy and entropy in both reaction directions that catalyzed by SAK were lower than those catalyzed by EAK. The model structure of SAK showed the significantly reduced numbers of salt bridges and cation-pi interactions as compared with EAK. These results suggest that weakening of intramolecular electrostatic interactions of SAK is involved in a more flexible structure which is likely to be responsible for its cold adaptation.     

Structural,Genetic, and Functional Signatures of Disordered Neuro-Immunological Development in Autism Spectrum Disorder

Background

Numerous linkage studies have been performed in pedigrees of Autism Spectrum Disorders, and these studies point to diverse loci and etiologies of autism in different pedigrees. The underlying pattern may be identified by an integrative approach, especially since ASD is a complex disorder manifested through many loci.

Method

Autism spectrum disorder (ASD) was studied through two different and independent genome-scale measurement modalities. We analyzed the results of copy number variation in autism and triangulated these with linkage studies.

Results

Consistently across both genome-scale measurements, the same two molecular themes emerged: immune/chemokine pathways and developmental pathways.

Conclusion

Linkage studies in aggregate do indeed share a thematic consistency, one which structural analyses recapitulate with high significance. These results also show for the first time that genomic profiling of pathways using a recombination distance metric can capture pathways that are consistent with those obtained from copy number variations (CNV).     

Glutathione Synthetase of Aspergillus niger: Structural Properties of the Enzyme in Prokaryotes and Eukaryotes

Glutathione synthetase isolated from a mold, Aspergillus niger, had a molecular weight of 110,000 and consisted of two apparently identical subunits, each with a molecular weight of 55,000. The enzyme was most active at pH 8.5. It specifically utilized glycine and ATP, and required Mg^{2 +} or Mn^{2 +} for its catalytic function. A comparison of glutathione synthetases from various sources indicated that the enzyme of eukaryotes (mammals, molds and yeasts) differ from those of prokaryotes {Escherichia coli B and Proteus mirabilis) in molecular structure, although the enzymes from both types of organisms contain an active site thiol and catalyze the same reaction.     

Thermal Adaptation of Viruses and Bacteria

A previously established multiscale population genetics model posits that fitness can be inferred from the physical properties of proteins under the physiological assumption that a loss of stability by any protein confers the lethal phenotype to an organism. Here, we develop this model further by positing that replication rate (fitness) of a bacterial or viral strain directly depends on the copy number of folded proteins, which determine its replication rate. Using this model, and both numerical and analytical approaches, we studied the adaptation process of bacteria and viruses at varied environmental temperatures. We found that a broad distribution of protein stabilities observed in the model and in experiment is the key determinant of thermal response for viruses and bacteria. Our results explain most of the earlier experimental observations: the striking asymmetry of thermal response curves; the absence of evolutionary tradeoff, which was expected but not found in experiments; correlation between denaturation temperature for several protein families and the optimal growth temperature of their carrier organisms; and proximity of bacterial or viral optimal growth temperatures to their evolutionary temperatures. Our theory quantitatively and with high accuracy described thermal response curves for 35 bacterial species using, for each species, only two adjustable parameters—the number of rate-determining genes and the energy barrier for metabolic reactions.     

Adaptation of the Thermal Responses of Insects

SYNOPSIS. Some insects adjust heat production and heat loss,while others depend upon adjustments in location and postureto regulate body temperature. Many activities oE insects aretuned to internal temperature. These two features predict thatthe nature and form of temperature control in insects interactstrongly in adaptation to climate, energy demand, niche specialization,and population size of insects.     

Homologies in the Structural Genes Coding for Sulphate Reducing Enzymes from Higher Plants and Prokaryotes*

The structural genes of enterobacteria encoding for the enzymes involved in the assimilatory reduction of sulphate (“cys genes”) were used in order to identify homologous genes from phototrophic cyanobacteria and higher plants. By Southern hybridisation of genomic DNA from the higher organisms with the cys DNA-probes derived from Escherichia coli, discrete restriction fragments were found in higher plants and in cyanobacteria indicating the occurrence of related DNA. Two of the cyanobacterial genes were cloned and identified by DNA and amino acid sequence comparison as the structural genes encoding the PAPS-reductase (EC 1.8.4.-) and the ferredoxin: sulphite-reductase (EC 1.8.7.1). The nucleic acid of both genes showed stretches of highly conserved bases in regions of the sequences which are regarded as the functionally important domains of the gene products.     

Prokaryotes in the Early Precambrian

Bacteria and biofilms are frequently preserved in the fossil record, they occur in many sedimentary and volcanogenic-sedimentary rocks. It is highly probable that they always participate in weathering, transfer of matter, sedimentation, and diagenesis of deposits.     

Functional and Structural Responses of a Degradative Microbial Community to Substrates with Varying Degrees of Complexity in Chemical Structure

Abstract The objective of the present study was to determine whether cultivation of a degradative community on substrates with varying degrees of chlorination and complexity in chemical structure, as well as cultivation in batch and flow cell culture, would alter the community's functional capability. The community was isolated from oil-contaminated soil and maintained in the laboratory on 2,4,6-trichlorobenzoic acid for 5 months before its ability to grow on 15 different chemicals as sole carbon source was evaluated in batch and flow cell systems. While the community could grow and develop biofilms in flow cells on all the substrates, only 11 of the 15 substrates could support growth in batch culture. Although biofilm development was less extensive on chemicals such as pentachlorophenol (2.09% average area covered by biofilm; average biofilm depth = 3 μm) than on 2,4,6-trichlorobenzoic acid (50.84% area covered; biofilm depth = 6.4 μm), no correlation was observed between the degree of chlorination, or number of rings, and the number of planktonic cells or biofilm biomass. In contrast, physicochemical characteristics such as the octanol/water partition coefficient had a significant effect on the development of biofilm biomass. In the case of planktonic communities, the degree of chlorination and ring number also had no effect on the BIOLOG carbon utilization profiles of the resulting communities. Although the sessile communities generally clustered separately from their planktonic counterparts, principal component analysis of carbon utilization profiles of the sessile communities showed different grouping between growth on chlorinated and nonchlorinated substrates. Analysis of the degradative community maintained on 2,4,6-trichlorobenzoic acid over an extended period further showed that adaptation to a new chemical environment is a rather slow process, since the substrate utilization profiles did not stabilize even after 12 months. These results demonstrate the flexibility in metabolic ability and community structure found in microbial communities. Received: 30 November 1998; Accepted: 19 May 1999