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Selection of bacteria capable of dissimilatory reduction of Fe(III) from a long-term continous culture on molasses and their use in a microbial fuel cell.
Get PDFFerric ion-respiring microorganisms (FRMs) are a group of prokaryotes that use iron (III) as well as other metals as terminal electron acceptors in the process of anaerobic respiration. Special attention is paid to a biotechnological significance of FRMs because of their potential role in electricity production in microbial fuel cells where the terminal acceptor of the electrons during anaerobic respiration is not a ferric ion but the anode. One of the best known FRMs is the Shewanellaceae family. Most of Shewanella species were isolated from marine environments.
In this report sugar beet molasses and ferric oxide were successfully used in the selection of a bacterial consortium capable of dissimilatory iron (III) reduction in a long-term continuous culture. The inoculum was a sample of eutrophic lake bottom sediment. Among the bacteria present in this culture were representatives of the Enterobacteriaceae, and the genera Pseudomonas and Shewanella. Two non-marine Fe(III)-reducing Shewanella-related clones named POL1 and POL2 were isolated. The ability of POL1 and POL2 isolates to metabolize a panel of 190 carbon sources were examined using a BIOLOG assay. The results confirmed the ability of shewanellas to utilize a broad range of carbon substrates. The utility of the POL1 and POL2 isolates in H-type MFCs operating on pyruvate or molasses was demonstrated. The operation of a MFC based on shewanellas cultured on molasses was shown for the first time. A novel two-stage character of the fuel cell polarizations, not previously noted in Shewanella MFC studies, was observed
Genetic Characterization of the CcpA-Dependent, Cellobiose-Specific PTS System Comprising CelB, PtcB and PtcA that Transports Lactose in Lactococcus lactis IL1403.
Get PDFLactose metabolism is one of the most important areas of research on Lactic Acid Bacteria (LAB). In rapidly acidifying industrial Lactococcus lactis strains, lactose is transported by a lactose-specific phosphotransferase system (PTS) encoded by a plasmid. However, an alternative lactose catabolic pathway was evidenced in the plasmid-cured, and thus initially lactose-negative L. lactis IL1403. We showed that in this strain the chromosomally-encoded cellobiose-specific PTS system comprising the celB, ptcB and ptcA genes is also able to transport lactose. By expression studies in the wild type IL1403 strain and IBB550, its ccpA-deficient derivative, we demonstrated that celB, ptcB and ptcA are tightly regulated by the general catabolite repression system, whereas celB additionally requires the presence of cellobiose to be fully induced. The comparison of expression levels of sugar catabolic genes indicated that the efficiency of CcpA-mediated catabolic repression depends on conservation of the cre sequence, and that in the case of perfect matching with the cre consensus, CcpA still drives a strong repression even under non-repressing conditions
Mapping of the interactions between partition proteins Delta and Omega of plasmid pSM19035 from Streptococcus pyogenes
Get PDFFormation of the segrosome, a nucleoprotein complex crucial for proper functioning of plasmid
partition systems, involves interactions between specific partition proteins (ParA-like and ParBlike),
ATP and specific DNA sequences (the centromeric sites). Although partition systems have
been studied for many years, details of the segrosome formation are not yet clear. Organization of
the pSM19035-encoded partition system is unique; in contrast with other known par systems,
here, the d and v genes do not constitute an operon. Moreover, Omega [a ParB-like protein which
has a Ribbon-Helix-Helix (RHH) structure] recognizes multiple centromeric sequences located in
the promoters of d, v and copS (copy-number control gene). The ParA-like protein Delta is a
Walker-type ATPase. In this work, we identify the interaction domains and requirements for
dimerization and hetero-interactions of the Delta and Omega proteins of pSM19035 plasmid. The
RHH structures are involved in Omega dimerization in vivo and its N-terminal unstructured part is
indispensable for association with Delta, both in vivo and in vitro. Omega does not need to form
dimers to interact with Delta. ATP binding is not required for Delta dimerization but is important for
interaction with Omega in vivo. The in vitro interaction between Delta and Omega depends on
ATP but does not require the presence of specific DNA segments (the centromere) recognized by
Omega. The C-terminal part of the Delta protein (aa 198–284) is indispensable for interaction
with Omega. Delta most probably interacts with Omega as a dimer since two amino acid
substitutions in a conserved region between the A9 and B motifs abolish both the dimerization of
Delta and its interaction with Omega
The human Suv3 helicase interacts with replication protein A and flap endonuclease 1 in the nucleus
Get PDFThe human Suv3 helicase has been shown to be a major player in mitochondrial RNA surveillance and decay. In the present study we identify two new interaction partners of hSUV3: the RPA (replication protein A0 and FEN1 (flap endonuclease). Another single-strand-binding protein, mtSSB fails to affect hSUV3 activity. Flap endonuclease activity of FEN1 is stimulated by hSUV3 independenttly of flap length. SUV3 may play a significant role in nuclear DNA metabolism
Autosomal recessive dilated cardiomyopathy due to DOLK mutations results from abnormal dystroglycan O-mannosylation
Get PDFGenetic causes for autosomal recessive forms of dilated cardiomyopathy (DCM) are only rarely identified, although they are thought to contribute considerably to sudden cardiac death and heart failure, especially in young children. Here, we describe 11 young patients (5-13 years) with a predominant presentation of dilated cardiomyopathy (DCM). Metabolic investigations showed deficient protein N-glycosylation, leading to a diagnosis of Congenital Disorders of Glycosylation (CDG). Homozygosity mapping in the consanguineous families showed a locus with two known genes in the N-glycosylation pathway. In all individuals, pathogenic mutations were identified in DOLK, encoding the dolichol kinase responsible for formation of dolichol-phosphate. Enzyme analysis in patients' fibroblasts confirmed a dolichol kinase deficiency in all families. In comparison with the generally multisystem presentation in CDG, the nonsyndromic DCM in several individuals was remarkable. Investigation of other dolichol-phosphate dependent glycosylation pathways in biopsied heart tissue indicated reduced O-mannosylation of alpha-dystroglycan with concomitant functional loss of its laminin-binding capacity, which has been linked to DCM. We thus identified a combined deficiency of protein N-glycosylation and alpha-dystroglycan O-mannosylation in patients with nonsyndromic DCM due to autosomal recessive DOLK mutations
Adaptative Potential of the Lactococcus Lactis IL594 Strain Encoded in Its 7 Plasmids
Get PDFThe extrachromosomal gene pool plays a significant role both in evolution and in the environmental adaptation of bacteria. The L. lactis subsp. lactis IL594 strain contains seven plasmids, named pIL1 to pIL7, and is the parental strain of the plasmid-free L. lactis IL1403, which is one of the best characterized lactococcal strains of LAB. Complete nucleotide sequences of pIL1 (6,382 bp), pIL2 (8,277 bp), pIL3 (19,244 bp), pIL4 (48,979), pIL5 (23,395), pIL6 (28,435 bp) and pIL7 (28,546) were established and deposited in the generally accessible database (GeneBank). Nine highly homologous repB-containing replicons, belonging to the lactococcal theta-type replicons, have been identified on the seven plasmids. Moreover, a putative region involved in conjugative plasmid mobilization was found on four plasmids, through identification of the presence of mob genes and/or oriT sequences. Detailed bioinformatic analysis of the plasmid nucleotide sequences provided new insight into the repertoire of plasmid-encoded functions in L. lactis, and indicated that plasmid genes from IL594 strain can be important for L. lactis adaptation to specific environmental conditions (e.g. genes coding for proteins involved in DNA repair or cold shock response) as well as for technological processes (e.g. genes encoding citrate and lactose utilization, oligopeptide transport, restriction-modification system). Moreover, global gene analysis indicated cooperation between plasmid- and chromosome-encoded metabolic pathway
Revisiting the Yeast PPR Proteins - Application of an Iterative Hidden Markov Model Algorithm Reveals New Members of the Rapidly Evolving Family.
Get PDFPentatricopeptide repeat (PPR) proteins form the largest known RNA-binding protein family, and are found in all eukaryotes, being particularly abundant in higher plants. PPR proteins localize mostly to mitochondria and chloroplasts, and many were shown to modulate organellar genome expression on the posttranscriptional level. While the genomes of land plants encode hundreds of PPR proteins, only a few have been identified in Fungi and Metazoa. As the current PPR motif profiles are built mainly on the basis of the predominant plant sequences, they are unlikely to be optimal for detecting fungal and animal members of the family, and many putative PPR proteins in these genomes may remain undetected. In order to verify this hypothesis we designed a HMM-based bioinformatic tool called SCIPHER (Supervised Clustering-based Iterative Phylogenetic Hidden Markov Model algorithm for the Evaluation of tandem Repeat motif families) using sequence data from orthologous clusters from available yeast genomes. This approach allowed us to assign twelve new proteins in S. cerevisiae to the PPR family. Similarly, in other yeast species we obtained a five-fold increase in the detection of PPR motifs, compared to the previous tools. All the newly identified S. cerevisiae PPR proteins localize in the mitochondrion and are a part of the RNA processing interaction network. Furthermore, the yeast PPR proteins seem to undergo an accelerated divergent evolution. Analysis of single and double amino acid substitutions in the Dmr1 protein of S. cerevisiae suggests that cooperative interactions between motifs and pseudoreversion could be the force driving this rapid evolution
Molekularne mechanizmy oporności bakterii kwasu mlekowego na bakteriofagi.
Get PDFLactic acid bacteria (LAB) constitute a heterogeneous group of bacteria, which are found in diverse environments, such as the human body or plants, and are traditionally used to produce fermented food. Food bio-transformation in industrial processes increases the economical importance of LAB. However, conditions that exist in industrial facilities do not seem to be an optimal environment for bacteria. During technological processes, which take place in enclosed space, the intensity of physical (temperature shift), chemical (acids) or biological (phages) stress factors raises dramatically. In the dairy industry, bacteriophage contamination is regarded as a serious problem due to the disturbance or arrest of the production processes, which results in significant economical losses. It is well documented that LAB evolved defense systems against bacteriophages, which allow them to survive in harsh conditions. Therefore, bacteria used in food industry are selected for high level of bacteriophage resistance. According to the mode of action, natural bacterial defense systems against their predators were divided into 5 categories: (i) inhibition of phage adsorption, (ii) blocking of phage DNA injection, (iii) phage abortive infection systems, (iv) restriction modification systems, (v) CRISPR/Cas systems. Remarkably, the majority of known bacteriophage resistance systems are plasmid-encoded. In this context, future studies on phage resistance mechanisms as well as plasmid sequencing may have an impact on solving the problem of phage infections in the dairy industry
Identification and functional analysis of Joka2, a tobacco member of the family of selective autophagy cargo receptors
Get PDFTwo main mechanisms of protein turnover exist in eukaryotic cells: the ubiquitin-proteasome system and the autophagylysosomal pathway. Autophagy is an emerging important constituent of many physiological and pathological processes, such as response to nutrient deficiency, programmed cell death and innate immune response. In mammalian cells the selectivity of autophagy is ensured by the presence of cargo receptors, such as p62/SQSTM1 and NBR1, responsible for sequestration of the ubiquitinated proteins. In plants no selective cargo receptors have been identified yet. The
present report indicates that structural and functional homologs of p62 and NBR1 proteins exist in plants. The tobacco protein, named Joka2, has been identified in yeast two-hybrid search as a binding partner of a small coiled-coil protein, a member of UP9/LSU family of unknown function, encoded by the UP9C gene strongly and specifically induced during sulfur deficiency. The typical domains of p62 and NBR1 are conserved in Joka2. Similarly to p62, Joka2-YFP has dual
localization (cytosolic speckles and the nucleus); it forms homodimers and interacts with a member of the ATG8 family.
Increased expression of Joka2 and ATG8f was observed in roots of tobacco plants grown for two days in nutrient-deficient conditions. Constitutive ectopic expression of Joka2-YFP in tobacco resulted in attenuated response (manifested by lesser yellowing of the leaves) to nutrient deficiency. In conclusion, Joka2, and presumably the process of selective autophagy, might constitute an important part of plant response to environmental stresses
Two-year follow-up of Sanfilippo Disease patients treated with a genistein-rich isoflavone extract: Assessment of effects on cognitive functions and general status of patients
Get PDFMucopolysaccharidoses (MPS) are inherited metabolic disorders caused by deficiencies in enzymes involved in degradation of glycosaminoglycans. MPS type III (Sanfilippo disease) is clinically characterized mainly by progressive and severe behavioral disturbances and cognitive dysfunction. Recent 1-year experimental treatment of 10 patients with a genistein (4’, 5, 7-trihydroxyisoflavone)-rich extract resulted in improvement of tested parameters, including cognitive and behavioral functions.Eight pediatric patients with Sanfilippo disease were enrolled into the study. The modified version of the Brief Assessment Examination was used to assess cognitive functions. Moreover, 18 different parameters concerning changes in conditions of patients were assessed by their parents.During the first year of the treatment, an improvement of cognitive functions in 7 patients and stabilization in 1 patient were assessed, while after the third year (2-year follow-up) further improvement was observed in 2 patients, stabilization in 3 patients and some deterioration in 3 patients. Monitoring of general and behavioral symptoms revealed improvement in all patients after the first year of the treatment, further improvement in 5 patients, and deterioration in 3 patients during
the next 2 years. We conclude that the treatment of Sanfilippo patients with a genistein-rich soy isoflavone extract(called gene expression-targeted isoflavone therapy[GET IT]) may be effective in either inhibition (in some patients) or slowing down (in other patients) of behavioral and cognitive problems over a longer period. An increased dose of genistein may improve the efficacy of the treatment