| 1. |
- Andersson, Jan O
(författare)
-
Evolution of Patchily Distributed Proteins Shared between Eukaryotes and Prokaryotes : Dictyostelium as a Case Study
- 2011
-
Ingår i: Journal of Molecular Biology and Biotechnology. - : S. Karger AG. - 1464-1801 .- 1660-2412. ; 20:2, s. 83-95
-
Tidskriftsartikel (refereegranskat)abstract
- Protein families are often patchily distributed in the tree of life; they are present in distantly related organisms, but absent in more closely related lineages. This could either be the result of lateral gene transfer between ancestors of organisms that encode them, or losses in the lineages that lack them. Here a novel approach is developed to study the evolution of patchily distributed proteins shared between prokaryotes and eukaryotes. Proteins encoded in the genome of cellular slime mold Dictyostelium discoideum and a restricted number of other lineages, including at least one prokaryote, were identified. Analyses of the phylogenetic distribution of 49 such patchily distributed protein families showed conflicts with organismal phylogenies; 25 are shared with the distantly related amoeboflagellate Naegleria (Excavata), whereas only two are present in the more closely related Entamoeba. Most protein families show unexpected topologies in phylogenetic analyses; eukaryotes are polyphyletic in 85% of the trees. These observations suggest that gene transfers have been an important mechanism for the distribution of patchily distributed proteins across all domains of life. Further studies of this exchangeable gene fraction are needed for a better understanding of the origin and evolution of eukaryotic genes and the diversification process of eukaryotes.
|
|
| 2. |
- Ausmees, Nora
(författare)
-
Intermediate filament-like cytoskeleton of Caulobacter crescentus
- 2006
-
Ingår i: Journal of Molecular Microbiology and Biotechnology. - : S. Karger AG. - 1464-1801. ; 11:3-5, s. 152-158
-
Tidskriftsartikel (refereegranskat)abstract
- Eukaryotic cytoskeleton consists of three main types of filaments: actin microfilaments, microtubules and intermediate filaments (IFs). Actin and tubulin-like proteins are also found in bacteria where they perform diverse cytoskeletal functions. IFs, however, are considered to be a characteristic constituent of metazoan cells only, where they (among other functions) are involved in determination and maintenance of cell shape and cellular integrity. Surprisingly, a coiled coil-rich protein called crescentin was recently shown to play a key role in determining the complex curved and helical cell shapes of the bacterium Caulobacter crescentus, and to exhibit several characteristic properties of animal IF proteins. First, the arrangement of the coiled coil domains of crescentin closely resembles the tripartite molecular architecture of IF proteins. Second, crescentin also possesses the defining biochemical property of IF proteins to assemble into 10-nm-wide filaments in vitro without cofactors. Furthermore, crescentin forms a higher-order helical structure in vivo, which is localized asymmetrically along the concave side of the cell. In close association with the cell membrane, the crescentin structure promotes the helical growth of the cell and thereby determines a curved or a helical shape, depending on the length of the cell. The unexpected finding of an IF-like element in a bacterium raises several interesting questions concerning, for example, the molecular mechanisms whereby complex and asymmetric cell shapes are generated by different bacteria, or the functional and evolutionary relatedness of crescentin to animal IF proteins.
|
|
| 3. |
- Fagerlind, Magnus, et al.
(författare)
-
The Role of Regulators in the Expression of Quorum-Sensing Signals in Pseudomonas aeruginosa
- 2003
-
Ingår i: Journal of Molecular Microbiology and Biotechnology. - : S. Karger. - 1464-1801. ; 6:2, s. 88-100
-
Tidskriftsartikel (refereegranskat)abstract
- Quorum-sensing systems provide Pseudomonas aeruginosa with a sensitive regulatory mechanism that allows for the induction of several phenotypic genes in a cell density fashion. In this work, a mathematical model of the acylated homoserine lactones regulatory network system in P. aeruginosa has been developed. It is the first integrated model to consider both quorum-sensing systems. The model has allowed us to disentangle the complex behavior exhibited by the system as the concentration of extracellular OdDHL is increased. At either low or high levels of extracellular OdDHL, the bacterium remains in an uninduced or induced state, respectively. At moderate levels, the behavior is characterized by several states. Here, the bacteria can switch suddenly from an uninduced to an induced phenotype in response to small changes in the concentration of extracellular OdDHL. Additionally, we have been able to address the roles of RsaL and Vfr as regulators of the quorum-sensing system. An important result from this analysis suggests that RsaL will increase the concentration of extracellular OdDHL required to induce the system, and it is a key regulator of the inhibition of the quorum-sensing system under low cell densities. Most importantly, our results suggest that Vfr has strong regulatory effects on the system as an increased affinity between the LasR/OdDHL complex, and the lasR promoter leads to significant qualitative changes in induction patterns. We also show experimental data that demonstrate that Vfr is required for signal production in the early phase of growth, but that in the latter stages of growth, the vfr mutant is able to synthesize wild-type levels of signal.
|
|
| 4. |
- Gustafsson, Erik, et al.
(författare)
-
Characterizing the dynamics of the quorum-sensing system in Staphylococcus aureus
- 2004
-
Ingår i: Journal of molecular microbiology and biotechnology. - : S. Karger AG. - 1464-1801. ; 8:4, s. 232-242
-
Tidskriftsartikel (refereegranskat)abstract
- The virulence determinants of <i>Staphylococcus aureus</i> are expressed in a growth phase-dependent manner governed by the autoinducible quorum-sensing system <i>agr</i>. Activation of the <i>agr</i> system results in a rapid increase in the regulator RNAIII and occurs in response to accumulation of AIP. In order to activate the <i>agr</i> system, a basal transcription of <i>agr</i> components must be assumed. This basal transcription of <i>agr</i> components seems to be stimulated by <i>sarA</i>. To better understand how SarA would affect activation of the <i>agr</i> system by modulating the basal <i>agr</i> activity, a mathematical model for autoactivation of the <i>agr</i> system was set up. The model predicted that the <i>agr</i> system is hysteretic, meaning that the <i>agr</i> system is activated at a specific concentration of autoinducing peptide (AIP), whereas it is inactivated at a specific lower concentration of AIP. According to the model, changing the basal <i>agr</i> activity only had a marginal effect on steady-state levels of RNAIII but changed the sensitivity of the cells to AIP. This was supported by Northern blot analysis of RNAIII in <i>S. aureus</i> mutants with different levels of SarA expression. Since natural antagonistic AIPs have been demonstrated, the effect of adding inhibitors to the system was analyzed.
|
|
| 5. |
- Karlsson, Magnus, et al.
(författare)
-
Evolution of Family 18 Glycoside Hydrolases: Diversity, Domain Structures and Phylogenetic Relationships
- 2009
-
Ingår i: Journal of Molecular Microbiology and Biotechnology. - : S. Karger AG. - 1464-1801 .- 1475-3774. ; 16, s. 208-223
-
Tidskriftsartikel (refereegranskat)abstract
- Chitin and its derivates have many industrial and medical uses. There is a demand for chitin-modifying enzymes with new or modified properties and as microorganisms are the primary degraders of chitin in the environment, they provide a source of chitin-modifying enzymes with novel properties. We have analyzed the diversity, domain structure and phylogenetic relationships between family 18 chitinases based on complete genome sequences of bacteria, archaea, viruses, fungi, plants and animals. Our study shows that family 18 chitinases are divided into three main clusters, A, B and C. Clusters A and B both contain family 18 chitinases from bacteria, fungi and plants, suggesting that the differentiation of cluster A and B chitinases preceded the appearance of the eukaryotic lineage. Subgroups within clusters can have specific domain structures, as well as specific amino acid replacements in catalytic sites, which imply functional adaptation. This work provides a comprehensive overview of the evolutionary relationships of family 18 chitinases and provides a context for further investigations on functional aspects of family 18 chitinases in ecology and biotechnology. Copyright (C) 2008 S. Karger AG, Basel
|
|
| 6. |
- Kulyte, A, et al.
(författare)
-
Inhibition of Mycobacterium smegmatis gene expression and growth using antisense peptide nucleic acids
- 2005
-
Ingår i: Journal of molecular microbiology and biotechnology. - : S. Karger AG. - 1464-1801. ; 9:2, s. 101-109
-
Tidskriftsartikel (refereegranskat)abstract
- Antisense agents that inhibit genes at the mRNA level are attractive tools for genome-wide studies and drug target validation. The approach may be particularly well suited to studies of bacteria that are difficult to manipulate with standard genetic tools. Antisense peptide nucleic acids (PNA) with attached carrier peptides can inhibit gene expression in <i>Escherichia coli </i>and<i> Staphylococcus aureus</i>. Here we asked whether peptide-PNAs could mediate antisense effects in <i>Mycobacterium smegmatis</i>. We first targeted the <i>gfp</i> reporter gene and observed dose- and sequence-dependent inhibition at low micromolar concentrations. Sequence alterations within both the PNA and target mRNA sequences eliminated inhibition, strongly supporting an antisense mechanism of inhibition. Also, antisense PNAs with various attached peptides showed improved anti-<i>gfp</i> effects. Two peptide-PNAs targeted to the essential gene <i>inhA</i> were growth inhibitory and caused cell morphology changes that resemble that of InhA-depleted cells. Therefore, antisense peptide-PNAs can efficiently and specifically inhibit both reporter and endogenous essential genes in mycobacteria.
|
|
| 7. |
- Lewin, Anna, et al.
(författare)
-
Positively Regulated Glycerol/G3P-Dependent Bacillus subtilis Gene Expression System Based on Anti-Termination.
- 2009
-
Ingår i: Journal of Molecular Microbiology and Biotechnology. - : S. Karger AG. - 1464-1801. ; 17, s. 61-70
-
Tidskriftsartikel (refereegranskat)abstract
- Plasmid pLALA was constructed for glycerol or glycerol-3-phosphate inducible plasmid-borne gene expression in Bacillus subtilis and closely related Gram-positive bacteria. Gene expression using pLALA is based on anti-termination of transcription and involves the B. subtilis GlpP protein that in the presence of glycerol-3-phosphate acts as an anti-terminator protein by binding to the 5'-untranslated region of glpD mRNA. Properties and the usefulness of the system, denoted LALA, were validated by inducible production in B. subtilis strainsof two water-soluble proteins (beta-galactosidase and a protein phospho-tyrosine phosphatase), and one integral membrane protein (heme A synthase). Advantages with LALA is that it is based on positive control, does not involve a DNA-binding protein, and that glycerol, a cheap and stable compound, can be used as inducer of gene expression.
|
|
| 8. |
- Lorca, G L, et al.
(författare)
-
Characterization of the protein-synthesis dependent adaptive acid tolerance response in Lactobacillus acidophilus
- 2002
-
Ingår i: Journal of Molecular Microbiology and Biotechnology. - 1464-1801. ; 4:6, s. 525-532
-
Tidskriftsartikel (refereegranskat)abstract
- Exposure of L. acidophilus CRL 639 cells to sublethal adaptive acid conditions (pH 5.0 for 60 min) was found to confer protection against subsequent exposure to lethal pH (pH 3.0). Adaptation, which only occurred in complex media, was dependent on de novo protein synthesis and was inhibited by amino acid analogues. There was no modification in the protein synthesis rate during adaptation, but the protein degradation rate decreased. Synthesis of acid stress proteins may increase the stability of pre-existing proteins. By 2D-PAGE, induction of nine acid stress proteins and repression of several housekeeping proteins was observed. Putative heat shock proteins DnaK, DnaJ, GrpE, GroES and GroEL (70, 43, 24, 10 and 55 kDa, respectively) were among the proteins whose synthesis was induced in response to acid adaptation.
|
|
| 9. |
- Solem, C., et al.
(författare)
-
Phosphoglycerate Mutase Is a Highly Efficient Enzyme without Flux Control in Lactococcus lactis
- 2010
-
Ingår i: Journal of Molecular Microbiology and Biotechnology. - : S. Karger AG. - 1464-1801 .- 1475-3774. ; 18:3, s. 174-180
-
Tidskriftsartikel (refereegranskat)abstract
- The glycolytic enzyme phosphoglycerate mutase (PGM), which catalyzes the conversion of 3-phosphoglycerate to 2-phosphoglycerate, was examined in Lactococcus lactis with respect to its function, kinetics and glycolytic flux control. A library of strains with PGM activities ranging between 15-465% of the wild-type level was constructed by replacing the native promoter of pgm with synthetic promoters of varying strengths. The specific growth rate and glucose flux were found to be maximal at the wild-type level at which PGM had no flux control. Low flux control of PGM was found on mixed acid fluxes at highly reduced PGM activities. At the wild-type level PGM operated very far from V-max. Consequently, in a strain with only 15% PGM activity, the catalytic rate of PGM was almost six times higher than in the wildtype. K-m of PGM for 3-phosphoglycerate was 1.0 m M and k(cat) was 3,200 s(-1). The L. lactis PGM was dependent on 2,3-bisphosphoglyceric acid for activity, which showed that the enzyme is of the dPGM type in accordance with its predicted homology to dPGM enzymes from other organisms. In conclusion, PGM from L. lactis is a highly efficient catalyst, which partially explains why this enzyme has limited control in wild-type L. lactis. Copyright (C) 2010 S. Karger AG, Basel
|
|
| 10. |
- Yuan, Ming, et al.
(författare)
-
Interaction between the Yersinia tyrosine phosphatase YopH and its macrophage substrate, Fyn-binding protein, Fyb
- 2005
-
Ingår i: Journal of Molecular Biology and Biotechnology. - Wymondham, Norfolk : Horizon Scientific Press. - 1464-1801 .- 1660-2412. ; 9:3-4, s. 214-223
-
Tidskriftsartikel (refereegranskat)abstract
- Pathogenic Yersinia species can evade phagocytosis by injecting virulence effectors that interfere with the phagocytic machinery of host cells. One of these virulence effectors is the protein tyrosine phosphatase YopH. Through its enzymatic activity, YopH interferes with the initial phagocytic process by affecting signalling for cytoskeletal rearrangements. Fyb (Fyn-binding protein), which is an immune cell-specific adaptor protein, has been identified as a substrate of YopH in macrophages. In this study, the interaction between YopH and Fyb is studied. We show that YopH binds to Fyb via different regions in both phosphotyrosine-dependent and phosphotyrosine-independent ways. The phosphotyrosine substrate binding N-terminal part (1-130) of YopH as well as the C-terminal catalytic region binds to Fyb in a phosphotyrosine-dependent manner. We also show that a central part of YopH (130-260) interacts with the Fyb C-terminus (548-783) in a phosphotyrosine-independent manner. Further, we demonstrate that the N-terminal binding region of YopH is important for YopH-mediated functions on macrophages such as dephosphorylation of Fyb, blockage of phagocytosis, and cytotoxic effects. Copyright (c) 2005 S. Karger AG, Basel.
|
|
