Comparative genome analysis of Lactobacillus reuteri and Lactobacillus fermentum reveal a genomic island for reuterin and cobalamin production

Lactobacillus reuteri is a heterofermentative lactic acid bacterium that naturally inhabits the gut of humans and other animals. The probiotic effects of L. reuteri have been proposed to be largely associated with the production of the broad-spectrum antimicrobial compound reuterin during anaerobic metabolism of glycerol. We determined the complete genome sequences of the reuterin-producing L. reuteri JCM 1112(T) and its closely related species Lactobacillus fermentum IFO 3956. Both are in the same phylogenetic group within the genus Lactobacillus. Comparative genome analysis revealed that L. reuteri JCM 1112(T) has a unique cluster of 58 genes for the biosynthesis of reuterin and cobalamin (vitamin B(12)). The 58-gene cluster has a lower GC content and is apparently inserted into the conserved region, suggesting that the cluster represents a genomic island acquired from an anomalous source. Two-dimensional nuclear magnetic resonance (2D-NMR) with (13)C(3)-glycerol demonstrated that L. reuteri JCM 1112(T) could convert glycerol to reuterin in vivo, substantiating the potential of L. reuteri JCM 1112(T) to produce reuterin in the intestine. Given that glycerol is shown to be naturally present in feces, the acquired ability to produce reuterin and cobalamin is an adaptive evolutionary response that likely contributes to the probiotic properties of L. reuteri.

Complete genome sequence of Finegoldia magna, an anaerobic opportunistic pathogen

Finegoldia magna (formerly Peptostreptococcus magnus), a member of the Gram-positive anaerobic cocci (GPAC), is a commensal bacterium colonizing human skin and mucous membranes. Moreover, it is also recognized as an opportunistic pathogen responsible for various infectious diseases. Here, we report the complete genome sequence of F. magna ATCC 29328. The genome consists of a 1 797 577 bp circular chromosome and an 189 163 bp plasmid (pPEP1). The metabolic maps constructed based on the genome information confirmed that most F. magna strains cannot ferment most sugars, except fructose, and have various aminopeptidase activities. Three homologs of albumin-binding protein, a known virulence factor useful for antiphagocytosis, are encoded on the chromosome, and one albumin-binding protein homolog is encoded on the plasmid. A unique feature of the genome is that F. magna encodes many sortase genes, of which substrates may be involved in bacterial pathogenesis, such as antiphagocytosis and adherence to the host cell. The plasmid pPEP1 encodes seven sortase and seven substrate genes, whereas the chromosome encodes four sortase and 19 substrate genes. These plasmid-encoded sortases may play important roles in the pathogenesis of F. magna by enriching the variety of cell wall anchored surface proteins.

Genome-wide analysis of Chlamydophila pneumoniae gene expression at the late stage of infection

Chlamydophila pneumoniae, an obligate intracellular eubacterium, changes its form from a vegetative reticulate body into an infectious elementary body during the late stage of its infection cycle. Comprehension of the molecular events in the morphological change is important to understand the switching mechanism between acute and chronic infection, which is deemed to relate to the pathogenesis of atherosclerosis. Herein, we have attempted to screen genes expressed in the late stage with a genome-wide DNA microarray, resulting in nomination of 17 genes as the late-stage genes. Fourteen of the 17 genes and six other genes predicted as late-stage genes were confirmed to be up-regulated in the late stage with a quantitative reverse transcriptase–polymerase chain reaction. These 20 late-stage genes were classified into two groups by clustering analysis: ‘drastically induced’ and ‘moderately induced’ genes. Out of eight drastically induced genes, four contain σ²⁸ promoter-like sequences and the other four contain an upstream common sequence. It suggests that besides σ²⁸, there are certain up-regulatory mechanisms at the late stage, which may be involved in the chlamydial morphological change and thus pathogenesis.

Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes

Numerous microbes inhabit the human intestine, many of which are uncharacterized or uncultivable. They form a complex microbial community that deeply affects human physiology. To identify the genomic features common to all human gut microbiomes as well as those variable among them, we performed a large-scale comparative metagenomic analysis of fecal samples from 13 healthy individuals of various ages, including unweaned infants. We found that, while the gut microbiota from unweaned infants were simple and showed a high inter-individual variation in taxonomic and gene composition, those from adults and weaned children were more complex but showed a high functional uniformity regardless of age or sex. In searching for the genes over-represented in gut microbiomes, we identified 237 gene families commonly enriched in adult-type and 136 families in infant-type microbiomes, with a small overlap. An analysis of their predicted functions revealed various strategies employed by each type of microbiota to adapt to its intestinal environment, suggesting that these gene sets encode the core functions of adult and infant-type gut microbiota. By analysing the orphan genes, 647 new gene families were identified to be exclusively present in human intestinal microbiomes. In addition, we discovered a conjugative transposon family explosively amplified in human gut microbiomes, which strongly suggests that the intestine is a ‘hot spot’ for horizontal gene transfer between microbes.

Modified-dose capecitabine + bevacizumab for the treatment of advanced/metastatic hepatocellular carcinoma (HCC): A phase II, single-arm study

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Background: The oral fluoropyrimidine capecitabine (X; Xeloda®) has anti-tumor activity in metastatic colorectal, breast, gastric cancers and HCC. The humanized monoclonal antibody bevacizumab (A; Avastin®) targets VEGF and limits tumor angiogenesis. The combination of X+A is active in breast cancer xenografts and increases the objective response rate (ORR) in patients (pts) with anthracycline- and taxane-resistant breast cancer. X+A also appears to be highly active when administered with irinotecan as first-line treatment for metastatic colorectal cancer. We report data from a multicenter, Ensign’s 3-stage design, open-label phase II trial of X+A as first- line treatment for HCC. Methods: Pts with untreated, histologically confirmed advanced HCC received X 800mg/m2 orally bid d1–14 and A 7.5mg/kg i.v. infusion d1. Treatment was repeated q3w x6 cycles in the absence of disease progression or unacceptable toxicity. Pts without progressive disease after 6 cycles of X+A could continue on the same doses of X+A. Primary endpoint was ORR (RECIST); secondary endpoints were disease control rate, progression-free survival (PFS), overall survival, and safety. Results: 45 patients were enrolled. By Dec 2006 the 25 patients (male, 88%; median age 52 years; Child-Pugh A) enrolled in Stages 1 and 2 of the study had completed at least 6 months’ follow-up and were assessed for efficacy and safety. ORR (CR+PR) was 16% (95% CI 4.5–36.1%) and disease control rate (CR+PR+SD) was 60% (95% CI 38.7–78.9%). Median overall survival was 10.7 months (95% CI, 5.3–14.7) and median PFS was 4.1 months (95% CI, 1.6–6.2); the PFS rate (i.e. the event (PD or death) free rate) at 3 and 6 months was 64% (95% CI 45.2–82.8%) and 34% (95% CI 15.1- 53.2%), respectively. Median number of cycles per patient was 5 (range 1–6). The most common treatment-related grade 3 toxicities included hand-foot syndrome (n=2), nail changes (n=1), diarrhea (n=1), nausea/vomiting/hiccups (n=1), gastric ulcer hemorrhage (n=1). Conclusions: X+A appears to be both effective and well tolerated as first-line treatment for HCC, providing support for further evaluation of this combination in this difficult-to-treat cancer.

No significant financial relationships to disclose.

Increased foxp3+ regulatory T cells predicts for superior relapse-free and overall survival in early stage hepatocelullar carcinoma

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Background: Hepatocellular carcinoma (HCC) endemic in Asia is aggressive and mainly hepatitis B-related. In ovarian and breast cancer, higher levels of foxp3+ regulatory T cells predicts for a poorer clinical outcome. The reverse is true with follicular lymphoma and Hodgkin’s disease. We hypothesize that foxp3+ CD4+ regulatory T lymphocyte (Treg) frequency predicts for clinical outcome in HCC. We also examined the recently identified IL17-producing, RORγt-expressing, CD4+ pathogenic Th17 cells in HCC. Methods: We analyzed Treg cells (n=116) and CD8+ T cells (n=24) expression by CD3/Foxp3 double immunoenzymatic using a anti-Foxp3 murine monoclonal antibody (Nuffield Department of Clinical Laboratory Sciences, Oxford University, UK) and CD3/CD8 double immunofluorescence, respectively. Treg cells and CD8 cells expression were reported as a percentage of CD3+ T cells. RORγt (for Th17) and Foxp3 mRNA were measured using real-time PCR. Results: Median age (n=116) was 62 years, 65.5% were hepatitis B+ (n=76), 4.3% were hepatitis C+ (n=5), 1.7% were both hepatitis B+ and C+ (n=2) and 28.4% were not virus-related (n=33). Treg numbers were significantly higher in all 116 HCC (median 9.3% of CD3+ T cells) compared to paired adjacent liver (median 1.9%) (p<0.001). Conversely, CD8+ T cell numbers were significantly lower in 24 HCC (median 21.1%) vs paired liver (median 49.5%) (p<0.001). Stage 1 and II HCC patients (n=24) with superior overall survival (= 6 years) compared with stage I and II patients (n=29) with inferior survival (≤ 1 year) had a significantly higher Treg frequency (median 10.9% versus 8.4%) (p=0.035). Stage I and II HCC patients (n=66) who were relapse-free at ≥ 1 year vs Stage I and II HCC patients (n=21) who were relapse-free at ≤ 0.5 years had higher Treg frequency (median 10.2% vs 6.8%) (p = 0.005). Hepatitis B+ HCC patients (n=76) had significantly higher Treg (median 10.2%) compared to non-viral associated HCC patients (n=33) (p=0.013). No correlation was seen between ROR and foxp3 mRNA. ROR mRNA was over-expressed (> 1 fold) in 20 (54%) HCC (analysis ongoing). Conclusions: Treg expression was significantly higher in HCC compared to paired liver. Increased Treg frequency predicts for a superior relapse-free and overall survival in HCC.

No significant financial relationships to disclose.

The 160-kilobase genome of the bacterial endosymbiont Carsonella

Previous studies have suggested that the minimal cellular genome could be as small as 400 kilobases. Here, we report the complete genome sequence of the psyllid symbiont Carsonella ruddii, which consists of a circular chromosome of 159,662 base pairs, averaging 16.5% GC content. It is by far the smallest and most AT-rich bacterial genome yet characterized. The genome has a high coding density (97%) with many overlapping genes and reduced gene length. Genes for translation and amino acid biosynthesis are relatively well represented, but numerous genes considered essential for life are missing, suggesting that Carsonella may have achieved organelle-like status.

Genome Sequence of the Cat Pathogen, Chlamydophila felis

Chlamydophila felis (Chlamydia psittaci feline pneumonitis agent) is a worldwide spread pathogen for pneumonia and conjunctivitis in cats. Herein, we determined the entire genomic DNA sequence of the Japanese C. felis strain Fe/C-56 to understand the mechanism of diseases caused by this pathogen. The C. felis genome is composed of a circular 1,166,239 bp chromosome encoding 1005 protein-coding genes and a 7552 bp circular plasmid. Comparison of C. felis gene contents with other Chlamydia species shows that 795 genes are common in the family Chlamydiaceae species and 47 genes are specific to C. felis. Phylogenetic analysis of the common genes reveals that most of the orthologue sets exhibit a similar divergent pattern but 14 C. felis genes accumulate more mutations, implicating that these genes may be involved in the evolutional adaptation to the C. felis-specific niche. Gene distribution and orthologue analyses reveal that two distinctive regions, i.e. the plasticity zone and frequently gene-translocated regions (FGRs), may play important but different roles for chlamydial genome evolution. The genomic DNA sequence of C. felis provides information for comprehension of diseases and elucidation of the chlamydial evolution.

Massive genome erosion and functional adaptations provide insights into the symbiotic lifestyle of Sodalis glossinidius in the tsetse host

Sodalis glossinidius is a maternally transmitted endosymbiont of tsetse flies (Glossina spp.), an insect of medical and veterinary significance. Analysis of the complete sequence of Sodalis' chromosome (4,171,146 bp, encoding 2,432 protein coding sequences) indicates a reduced coding capacity of 51%. Furthermore, the chromosome contains 972 pseudogenes, an inordinately high number compared with that of other bacterial species. A high proportion of these pseudogenes are homologs of known proteins that function either in defense or in the transport and metabolism of carbohydrates and inorganic ions, suggesting Sodalis' degenerative adaptations to the immunity and restricted nutritional status of the host. Sodalis possesses three chromosomal symbiosis regions (SSR): SSR-1, SSR-2, and SSR-3, with gene inventories similar to the Type-III secretion system (TTSS) ysa from Yersinia enterolitica and SPI-1 and SPI-2 from Salmonella, respectively. While core components of the needle structure have been conserved, some of the effectors and regulators typically associated with these systems in pathogenic microbes are modified or eliminated in Sodalis. Analysis of SSR-specific invA transcript abundance in Sodalis during host development indicates that the individual symbiosis regions may exhibit different temporal expression profiles. In addition, the Sodalis chromosome encodes a complete flagella structure, key components of which are expressed in immature host developmental stages. These features may be important for the transmission and establishment of symbiont infections in the intra-uterine progeny. The data suggest that Sodalis represents an evolutionary intermediate transitioning from a free-living to a mutualistic lifestyle.

Whole genome sequence of Staphylococcus saprophyticus reveals the pathogenesis of uncomplicated urinary tract infection

Staphylococcus saprophyticus is a uropathogenic Staphylococcus frequently isolated from young female outpatients presenting with uncomplicated urinary tract infections. We sequenced the whole genome of S. saprophyticus type strain ATCC 15305, which harbors a circular chromosome of 2,516,575 bp with 2,446 ORFs and two plasmids. Comparative genomic analyses with the strains of two other species, Staphylococcus aureus and Staphylococcus epidermidis, as well as experimental data, revealed the following characteristics of the S. saprophyticus genome. S. saprophyticus does not possess any virulence factors found in S. aureus, such as coagulase, enterotoxins, exoenzymes, and extracellular matrix-binding proteins, although it does have a remarkable paralog expansion of transport systems related to highly variable ion contents in the urinary environment. A further unique feature is that only a single ORF is predictable as a cell wall-anchored protein, and it shows positive hemagglutination and adherence to human bladder cell associated with initial colonization in the urinary tract. It also shows significantly high urease activity in S. saprophyticus. The uropathogenicity of S. saprophyticus can be attributed to its genome that is needed for its survival in the human urinary tract by means of novel cell wall-anchored adhesin and redundant uro-adaptive transport systems, together with urease.

Patient skin dosimetry in haemodynamic and electrophysiology interventional cardiology

With the increase in number and complexity of interventional cardiology (IC) procedures, it is important to monitor skin dose in order to decrease skin injuries. This study investigated radiation doses for patients undergoing IC procedures, compare results with the literature and define a local dose-area product trigger level for operators to identify situations likely to exceed the threshold for transient skin erythema of 2 Gy. Dosimetric data were collected for 77 haemodynamic and 90 electrophysiological procedures. Mean maximum local skin doses (MSDs) were 0.28 Gy for coronary angiography, 1.03 Gy for percutaneous transluminal coronary angioplasty (PTCA), 0.03 Gy for pacemaker insertion, 0.17 Gy for radiofrequency ablation for nodal tachycardia, 0.10 Gy for WPW and 0.22 Gy for atrial flutter. Since MSD values for the other procedures were well below the deterministic effect limit, a trigger level of 140 Gy cm2 was derived for PTCA procedures alone.

Dose to cardiologists in haemodynamic and electrophysiology cardiac interventional procedures

Interventional cardiac procedures can be complex and involve extensive use of low dose rate fluoroscopy and high dose rate in image acquisition mode; hence, staff may receive significant radiation exposure. Radiation exposure to operators was assessed in 173 procedures. Fluoroscopy time, number of acquired images and dose-area product were recorded and occupational dose assessed with thermoluminescence dosemeters. The effective dose to the operator was compared with relevant literature data: values found were generally lower than those reported for other interventional cardiology laboratories. This is probably because of the strict radiation protection policy in our centre. Higher effective doses were found for defibrillator implantation and percutaneous transluminal coronary angiography procedures; for other cardiac procedures, effective dose was lower. Yearly extrapolated occupational doses to cardiologists are lower than the regulatory dose limit and in the lower band of doses reported in the literature.

Genomic analysis of Bacteroides fragilis reveals extensive DNA inversions regulating cell surface adaptation

Bacteroides are predominant human colonic commensals, but the principal pathogenic species, Bacteroides fragilis (BF), lives closely associated with the mucosal surface, whereas a second major species, Bacteroides thetaiotaomicron (BT), concentrates within the colon. We find corresponding differences in their genomes, based on determination of the genome sequence of BF and comparative analysis with BT. Both species have acquired two mechanisms that contribute to their dominance among the colonic microbiota: an exceptional capability to use a wide range of dietary polysaccharides by gene amplification and the capacity to create variable surface antigenicities by multiple DNA inversion systems. However, the gene amplification for polysaccharide assimilation is more developed in BT, in keeping with its internal localization. In contrast, external antigenic structures can be changed more systematically in BF. Thereby, at the mucosal surface, where microbes encounter continuous attack by host defenses, BF evasion of the immune system is favored, and its colonization and infectious potential are increased.

In silico inference of inclusion membrane protein family in obligate intracellular parasites chlamydiae

Chlamydiae are obligate intracellular pathogens that proliferate only inside a vacuole, called an inclusion. Chlamydial Inc proteins are known to be a major component of the inclusion membrane, but little is known about the gene number and function. The Inc proteins share very low sequence similarity but a similar hydropathy profile among them. Using the hydropathy profile, we computationally searched the open reading frames (ORFs) having a similar profile and predicted 90 and 36 ORFs (Inc-like ORFs) as candidates for Inc proteins in Chlamydia pneumoniae J138 and Chlamydia trachomatis serovar D, respectively. On the other hand, only a few Inc-like ORFs were found in organisms other than chlamydiae, suggesting that the Inc-like ORFs are specific to chlamydiae. Comparative genome analysis also revealed that the Inc-like ORFs have multiplied and diverged as paralogues and orthologues in the chlamydial genomes, and that some Inc-like ORFs lacked the N-terminal portion or encoded the split form. The data suggest that these gene products constitute a large protein family and may play an important role in chlamydial infection, growth and survival in the host cell.

System for automatically inferring a genetic netwerk from expression profiles

A system is constructed to automatically infer a genetic network byapplication of graphical Gaussian modeling to the expression profiledata. Our system is composed of two parts: one part is automaticdetermination of cluster boundaries of profiles in hierarchicalclustering, and another part is inference of a genetic network byapplication of graphical Gaussian modeling to the clustered profiles.Since thousands of or tens of thousands of gene expression profiles aremeasured under only one hundred conditions, the profiles naturally showsome similar patterns. Therefore, a preprocessing for systematicallyclustering the profiles is prerequisite to infer the relationship betweenthe genes. For this purpose, a method for automatic determination ofcluster boundaries is newly developed without any biological knowledgeand any additional analyses. Then, the profiles for each cluster areanalyzed by graphical Gaussian modeling to infer the relationship betweenthe clusters. Thus, our system automatically provides a graph betweenclusters only by input the profile data. The performance of the presentsystem is validated by 2467 profiles from yeast genes. The clusters andthe genetic network obtained by our system are discussed in terms of thegene function and the known regulatory relationship between genes.

Three novel repetitive units of reelin

Reelin is a protein involved in the organization of the developing brain of vertebrates. Reelin is divided into three parts, a F-spondin-like domain, a region including the epitopes of the monoclonal and polyclonal anti-Reelin antibodies, and eight-fold Reelin repeats. Reelin repeats consists of a subrepeat A, an EGF-like domain, and a subrepeat B. We found that the anti-Reelin antibodies' recognition region consists of three repetitive units. The correspondence of the repetitive units with the antigenicity is discussed.

Statistical estimation of cluster boundaries in gene expression profile data

MOTIVATION

Gene expression profile data are rapidly accumulating due to advances in microarray techniques. The abundant data are analyzed by clustering procedures to extract the useful information about the genes inherent in the data. In the clustering analyses, the systematic determination of the boundaries of gene clusters, instead of by visual inspection and biological knowledge, still remains challenging.

RESULTS

We propose a statistical procedure to estimate the number of clusters in the hierarchical clustering of the expression profiles. Following the hierarchical clustering, the statistical property of the profiles at the node in the dendrogram is evaluated by a statistics-based value: the variance inflation factor in the multiple regression analysis. The evaluation leads to an automatic determination of the cluster boundaries without any additional analyses and any biological knowledge of the measured genes. The performance of the present procedure is demonstrated on the profiles of 2467 yeast genes, with very promising results.

AVAILABILITY

A set of programs will be electronically sent upon request.

CONTACT

horimoto@post.saga-med.ac.jp; toh@beri.co.jp

Expansion of the zinc metallo-hydrolase family of the beta-lactamase fold

Recently, the zinc metallo-hydrolase family of the beta-lactamase fold has grown quite rapidly, accompanied by the accumulation of sequence and structure data. The variety of the biological functions of the family is higher than expected. In addition, the members often have mosaic structures with additional domains. The family includes class B beta-lactamase, glyoxalase II, arylsulfatase, flavoprotein, cyclase/dehydrase, an mRNA 3'-processing protein, a DNA cross-link repair enzyme, a DNA uptake-related protein, an alkylphosphonate uptake-related protein, CMP-N-acetylneuraminate hydroxylase, the romA gene product, alkylsulfatase, and insecticide hydrolases. In this minireview, the functional and structural varieties of the growing protein family are described.

Biochemical analysis of replication factor C from the hyperthermophilic archaeon Pyrococcus furiosus

Replication factor C (RFC) and proliferating cell nuclear antigen (PCNA) are accessory proteins essential for processive DNA synthesis in the domain Eucarya. The function of RFC is to load PCNA, a processivity factor of eukaryotic DNA polymerases delta and epsilon, onto primed DNA templates. RFC-like genes, arranged in tandem in the Pyrococcus furiosus genome, were cloned and expressed individually in Escherichia coli cells to determine their roles in DNA synthesis. The P. furiosus RFC (PfuRFC) consists of a small subunit (RFCS) and a large subunit (RFCL). Highly purified RFCS possesses an ATPase activity, which was stimulated up to twofold in the presence of both single-stranded DNA (ssDNA) and P. furiosus PCNA (PfuPCNA). The ATPase activity of PfuRFC itself was as strong as that of RFCS. However, in the presence of PfuPCNA and ssDNA, PfuRFC exhibited a 10-fold increase in ATPase activity under the same conditions. RFCL formed very large complexes by itself and had an extremely weak ATPase activity, which was not stimulated by PfuPCNA and DNA. The PfuRFC stimulated PfuPCNA-dependent DNA synthesis by both polymerase I and polymerase II from P. furiosus. We propose that PfuRFC is required for efficient loading of PfuPCNA and that the role of RFC in processive DNA synthesis is conserved in Archaea and Eucarya.

Mutational analysis of the Pyrococcus furiosus holliday junction resolvase hjc revealed functionally important residues for dimer formation, junction DNA binding, and cleavage activities

The Holliday junction cleavage protein, Hjc resolvase of Pyrococcus furiosus, is the first Holliday junction resolvase to be discovered in Archaea. Although the archaeal resolvase shares certain biochemical properties with other non-archaeal junction resolvases, no amino acid sequence similarity has been identified. To investigate the structure-function relationship of this new Holliday junction resolvase, we constructed a series of mutant hjc genes using site-directed mutagenesis targeted at the residues conserved among the archaeal orthologs. The products of these mutant genes were purified to homogeneity. With analysis of the activity of the mutant proteins to bind and cleave synthetic Holliday junctions, one acidic residue, Glu-9, and two basic residues, Arg-10 and Arg-25, were found to play critical roles in enzyme action. This is in addition to the three conserved residues, Asp-33, Glu-46, and Lys-48, which are also conserved in the motif found in the type II restriction endonuclease family proteins. Two aromatic residues, Phe-68 and Phe-72, are important for the formation of the homodimer probably through hydrophobic interactions. The results of these studies have provided insights into the structure-function relationships of the archaeal Holliday junction resolvase as well as the universality and diversity of the Holliday junction cleavage reaction.

Hjc resolvase is a distantly related member of the type II restriction endonuclease family

Hjc resolvase is an archaeal enzyme involved in homologous DNA recombination at the Holliday junction intermediate. However, the structure and the catalytic mechanism of the enzyme have not yet been identified. We performed database searching using the amino acid sequence of the enzyme from Pyrococcus furiosus as a query. We detected 59 amino acid sequences showing weak but significant sequence similarity to the Hjc resolvase. The detected sequences included DPN:II, HAE:II and Vsr endonuclease, which belong to the type II restriction endonuclease family. In addition, a highly conserved region was identified from a multiple alignment of the detected sequences, which was similar to an active site of the type II restriction endonucleases. We substituted three conserved amino acid residues in the highly conserved region of the Hjc resolvase with Ala residues. The amino acid replacements inactivated the enzyme. The experimental study, together with the results of the database searching, suggests that the Hjc resolvase is a distantly related member of the type II restriction endonuclease family. In addition, the results of our database searches suggested that the members of the RecB domain superfamily are evolutionarily related to the type II restriction endonuclease family.

Glycine-rich region of mitochondrial processing peptidase alpha-subunit is essential for binding and cleavage of the precursor proteins

Mitochondrial processing peptidase, a metalloendopeptidase consisting of alpha- and beta-subunits, specifically recognizes a large variety of mitochondrial precursor proteins and cleaves off amino-terminal extension peptides. The alpha-subunit has a characteristic glycine-rich segment in the middle portion. To elucidate the role of the region in processing functions of the enzyme, deletion or site-directed mutations were introduced, and effects on kinetic parameters and substrate binding of the enzyme were analyzed. Deletion of three residues of the region, Phe(289) to Ala(291), led to a dramatic reduction in processing activity to practically zero. Mutation of Phe(289), Lys(296), and Met(298) to alanine resulted in a decrease in the activity, but these mutations had no apparent effect on interactions between the two subunits, indicating that reduction in processing activity is not due to structural disruption at the interface interacting with the beta-subunit. Although the mutant enzymes, Phe289Ala, Lys296Ala, and Met298Ala, had an approximate 10-fold less affinity for substrate peptides than did that of the wild type, the deletion mutant, delta 289-291, showed an extremely low affinity. Thus, shortening of the glycine-rich stretch led to a dramatic reduction of interaction between the enzyme and substrate peptides and cleavage reaction, whereas mutation of each amino acid in this region seemed to affect primarily the cleavage reaction.