Surface layers of methanotrophic bacteria

Structural and functional characteristics of the regular glycoprotein layers in prokaryotes are analyzed with a special emphasis on aerobic methanotrophic bacteria. S-Layers are present at the surfaces of Methylococcus, Methylothermus, and Methylomicrobium cells. Different Methylomicrobium species either synthesize S-layers with planar (p2, p4) symmetry or form cup-shaped or conical structures with hexagonal (p6) symmetry. A unique, copper-binding polypeptide ‘CorA’/MopE (27/45 kDa), which is coexpressed with the diheme periplasmic cytochrome c peroxidase ‘CorB’/Mca (80 kDa) was found in Methylomicrobium album BG8, Methylomicrobium alcaliphilum 20Z, and Methylococcus capsulatus Bath. This tandem of the surface proteins is functionally analogous to a new siderophore: methanobactin. Importantly, no ‘CorA’/MopE homologue was found in methanotrophs not forming S-layers. The role of surface proteins in copper metabolism and initial methane oxidation is discussed.     

Structural and functional features of methanotrophs from hypersaline and alkaline lakes

Ten strains of aerobic methanotrophic bacteria represented by halophilic neutrophiles or halotolerant alkaliphiles were isolated from saline and alkaline lakes of southeast Siberia, Mongolia, Africa, and North America. Based on analysis of the nucleotide sequences of 16S rRNA gene and the pmoA gene encoding particulate methane monooxygenase, the isolates were classified as Methylomicrobium alcaliphilum, Methylomicrobium buryatense, and Methylobacter marinus. All strains of the genus Methylomicrobium were shown to synthesize glycoprotein S-layers located on the cell surface with hexagonal symmetry (p6) as a monolayer of cup-shaped structures or fine “inverted” conical structures and as plates consisting of protein subunits with inclined (p2) symmetry. During adaptation to the high salinity of the medium, isolated methanotrophs synthesize osmoprotectants: ectoine, sucrose, and glutamate. The ectC gene encoding ectoine synthase (EctC) was identified in six methanotrophic strains. Phylogenetic analysis of translated amino acid sequence of the ectC gene fragment suggests lateral transfer of the genes of ectoine synthesis as the most probable way for methanotrophs to acquire resistance to high external salinity.     

Isolation and taxonomic characterization of a novel type I methanotrophic bacterium

A methane-oxidizing bacterium was isolated from the effluent of manure and its molecular and biochemical properties were characterized. The isolate was aerobic, Gram-negative, and non-motile. The organism had a type I intracytoplasmic membrane structure and granular inclusion bodies. The outer cell wall surface (S-layers) was tightly packed with cup-shaped structures. Colonies were light yellow on nitrate mineral salt agar medium. In addition, the organism was catalase and oxidase positive. The isolate used the ribulose monophosphate (RuMP) pathway for carbon assimilation, and was able to utilize methane and methanol as a sole carbon and energy source, however, it could not utilize any other organic compounds that were tested. The cells grew well in a mixture of methane and air (methane:air=1:1, v/v) in a compulsory circulation diffusion system, and when grown under those conditions, the optimum pH was approximately 7.0 and the optimal temperature was 30 degrees. In addition, the specific growth rate and generation time were 0.13 per h and 5.43 h, respectively, when grown under the optimum conditions. The major ubiquinone was Q-8, and the G+C mol% of the DNA was 55.3. Phylogenetic analyses based on the 16S rRNA gene sequence comparisons showed that this bacterium belongs to a group of type I methanotrophs, and that it is most closely related to Methylomicrobium, with a sequence similarity of 99%. Therefore, the isolate was named Methylomicrobium sp. HG-1.     

Taxonomic characterization of new alkaliphilic and alkalitolerant methanotrophs from soda lakes of the Southeastern Transbaikal region and description of Methylomicrobium buryatense sp.nov

Five strains of obligate methanotrophic bacteria (4G, 5G, 6G, 7G and 5B) isolated from bottom sediments of Southeastern Transbaikal soda lakes (pH 9.5-10.5) are taxonomically described. These bacteria are aerobic, Gram-negative monotrichous rods having tightly packed cup-shaped structures on the outer cell wall surface (S-layers) and Type I intracytoplasmic membranes. All the isolates possess particulate methane monooxygenase (pMMO) and one strain (5G) also contains soluble methane monooxygenase (sMMO). They assimilate methane and methanol via the ribulose monophosphate pathway (RuMP). The isolates are alkalitolerant or facultatively alkaliphilic, able to grow at pH 10.5-11.0 and optimally at pH 8.5-9.5. These organisms are obligately dependent on the presence of sodium ions in the growth medium and tolerate up to 0.9-1.4 M NaCl or 1 M NaHCO3. Although being mesophilic, all the isolates are resistant to heating (80 degrees C, 20 min), freezing and drying. Their cellular fatty acids profiles primarily consist of C(16:1). The major phospholipids are phosphatidylethanolamine and phosphatidylglycerol. The main quinone is Q-8. The DNA G+C content ranges from 49.2-51.5 mol %. Comparative 16S rDNA sequencing showed that the newly isolated methanotrophs are related to membres of the Methylomicrobium genus. However, they differ from the known members of this genus by DNA-DNA relatedness. Based on pheno- and genotypic characteristics, we propose a new species of the genus Methylomicrobium Methylomicrobium buryatense sp. nov.     

Taxonomic Characterization of New Alkaliphilic and Alkalitolerant Methanotrophs from Soda Lakes of the Southeastern Transbaikal Region and description of Methylomicrobium buryatense sp.nov.

Five strains of obligate methanotrophic bacteria (4G, 5G, 6G, 7G and 5B) isolated from bottom sediments of Southeastern Transbaikal soda lakes (pH 9.5–10.5) are taxonomically described. These bacteria are aerobic, Gram-negative monotrichous rods having tightly packed cup-shaped structures on the outer cell wall surface (S-layers) and Type I intracytoplasmic membranes. All the isolates possess particulate methane monooxygenase (pMMO) and one strain (5G) also contains soluble methane monooxygenase (sMMO). They assimilate methane and methanol via the ribulose monophosphate pathway (RuMP). The isolates are alkalitolerant or facultatively alkaliphilic, able to grow at pH 10.5–11.0 and optimally at pH 8.5–9.5. These organisms are obligately dependent on the presence of sodium ions in the growth medium and tolerate up to 0.9–1.4 M NaCl or 1 M NaHCO₃. Although being mesophilic, all the isolates are resistant to heating (80 °C, 20 min), freezing and drying. Their cellular fatty acids profiles primarily consist of C_16:1. The major phospholipids are phosphatidylethanolamine and phosphatidylglycerol. The main quinone is Q-8. The DNA G+C content ranges from 49.2–51.5 mol%. Comparative 16S rDNA sequencing showed that the newly isolated methanotrophs are related to membres of the Methylomicrobium genus. However, they differ from the known members of this genus by DNA-DNA relatedness. Based on pheno- and genotypic characteristics, we propose a new species of the genus Methylomicrobium - Methylomicrobium buryatense sp. nov.     

Isolation of Intracytoplasmic Membrane from the Methanotrophic Bacterium Methylomicrobium album BG8

Methane-oxidizing bacteria, including Methylomicrobium album BG8, form an intracytoplasmic membrane in addition to the cytoplasmic and outer membranes of the cell envelope. Techniques to isolate the intracytoplasmic membrane of M. album BG8 were developed. An intracytoplasmic membrane fraction was separated from a cell envelope fraction on the basis of sedimentation velocity in sucrose density gradients. Proteins associated with the particulate methane monooxygenase were found in both membrane fractions. Received: 27 July 1999 / Accepted: 30 August 1999     

Characterization of Two EF‐hand Domain‐containing Proteins from Toxoplasma gondii

The universal role of calcium (Ca²⁺) as a second messenger in cells depends on a large number of Ca²⁺‐binding proteins (CBP), which are able to bind Ca²⁺ through specific domains. Many CBPs share a type of Ca²⁺‐binding domain known as the EF‐hand. The EF‐hand motif has been well studied and consists of a helix‐loop‐helix structural domain with specific amino acids in the loop region that interact with Ca²⁺. In Toxoplasma gondii a large number of genes (approximately 68) are predicted to have at least one EF‐hand motif. The majority of these genes have not been characterized. We report the characterization of two EF‐hand motif‐containing proteins, TgGT1_216620 and TgGT1_280480, which localize to the plasma membrane and to the rhoptry bulb, respectively. Genetic disruption of these genes by CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 (CRISPR‐associated protein 9) resulted in mutant parasite clones (Δtg216620 and Δtg280480) that grew at a slower rate than control cells. Ca²⁺ measurements showed that Δtg216620 cells did not respond to extracellular Ca²⁺ as the parental controls while Δtg280480 cells appeared to respond as the parental cells. Our hypothesis is that TgGT1_216620 is important for Ca²⁺ influx while TgGT1_280480 may be playing a different role in the rhoptries.     

Identification and characterization of two cleavage fragments from the <Emphasis Type="Italic">Aquareovirus</Emphasis> nonstructural protein NS80

Aquareovirus species vary with respect to pathogenicity, and the nonstructural protein NS80 of aquareoviruses has been implicated in the regulation of viral replication and assembly, which can form viral inclusion bodies (VIBs) and recruit viral proteins to its VIBs in infected cells. NS80 consists of 742 amino acids with a molecular weight of approximately 80 kDa. Interestingly, a short specific fragment of NS80 has also been detected in infected cells. In this study, an approximately 58-kDa product of NS80 was confirmed in various infected and transfected cells by immunoblotting analyses using α-NS80C. Mutational analysis and time course expression assays indicated that the accumulation of the 58-kDa fragment was related to time and infection dose, suggesting that the fragment is not a transient intermediate of protein degradation. Moreover, another smaller fragment with a molecular mass of approximately 22 kDa was observed in transfected and infected cells by immunoblotting with a specific anti-FLAG monoclonal antibody or α-NS80N, indicating that the 58- kDa polypeptide is derived from a specific cleavage site near the amino terminus of NS80. Additionally, different subcellular localization patterns were observed for the 22-kDa and 58-kDa fragments in an immunofluorescence analysis, implying that the two cleavage fragments of NS80 function differently in the viral life cycle. These results provide a basis for additional studies of the role of NS80 played in replication and particle assembly of the Aquareovirus.

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Improvement of antagonism and carbendazim tolerance in native Trichoderma isolates through ethyl methane sulfonate (EMS) mutagenesis

Genetic enhancement of TCT₄ and TCT₁₀ was aimed in the present paper. Trichoderma reesei (TCT₁₀/M₁₈) mutant isolate evolved by ethyl methane sulfonate mutations was found to exhibit altered properties compared to its parent isolates. This mutant grew well in the potato dextrose agar (PDA) medium containing carbendazim (50 ppm). RAPD-PCR results suggested the uniqueness of mutants, which was useful in differentiating mutant and wild Trichoderma isolates. These mutants established well in the rhizosphere of rough lemon seedlings. The seedlings treated with carbendazim followed by an application of carbendazim-resistant mutant (TCT₁₀/M₁₈) resulted in a better seedling emergence and a less dry root rot disease caused by Fusarium solani in nursery conditions.     

曼陀罗培养细胞的硝酸还原酶突变株

经紫外诱变氯酸钾筛选,得到一个低硝酸还原酶(NADH:硝酸氧化还原酶.EC1.6.6.1.,以下简写为NR)活力的细胞株。其主要特征:NR活力低,约为正常型的1/5;对氯酸钾具有较强的抗性;不适合在单纯以硝酸盐为氮源的培养基上生长,能在以(NH_4)_2SO_4为唯一氮源的培养基上生长。蛋白电泳表明,此细胞株与正常型有不同的蛋白带。这些特征在没有选择压力的培养基上培养二年后,仍保持不变,说明此细胞株是一个遗传型的变异株。     

Outer membrane proteins of Methylococcus capsulatus (Bath)

Membranes obtained from whole-cell lysates of Methylococcus capsulatus (Bath) were separated by Triton X-100 extraction. The resulting insoluble fraction was enriched in outer membranes as assessed by electron microscopy and by the content of β-hydroxy palmitic acid and particulate methane monooxygenase. Major proteins with molecular masses of approximately 27, 40, 46, 59, and 66 kDa were detected by SDS-PAGE of the Triton-X-100-insoluble membranes. MopA, MopB, MopC, MopD, and MopE (Methylococcus outer membrane protein) are proposed to designate these proteins. Several of the Mop proteins exhibited heat-modifiable properties in SDS-PAGE and were influenced by the presence of 2-mercaptoethanol in the sample buffer. The 46- and 59-kDa bands migrated as a single high-molecular-mass 95-kDa oligomer under mild denaturing conditions. When reconstituted into black lipid membranes, this oligomer was shown to serve as a channel with an estimated single-channel conductance of 1.4 nS in 1 M KCl. Received: 20 December 1996 / Accepted: 11 April 1997     

Construction and characterization of a clostripain-like protease-deficient mutant of <Emphasis Type="Italic">Clostridium perfringens</Emphasis> as a strain for clostridial gene expression

The inherent difficulty of expressing clostridial AT-rich genes in a heterologous host has limited their biotechnological application. We previously reported a plasmid for high-level expression of clostridial genes in Clostridium perfringens (Takamizawa et al., Protein Expr Purif 36:70–75, 2004). In this study, we examined the extracellular proteases of C. perfringens strain 13. Zymographic analysis and caseinase assaying of a culture supernatant showed that it contained a protease activated by dithiothreitol and Ca²⁺, suggesting that clostripain-like protease (Clp) is the most likely candidate for the major extracellular protease. Disruption of the clp gene by homologous recombination markedly decreased the level of caseinase activity in the culture supernatant. Analysis by sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS-PAGE) revealed that the Clp⁻ mutant but not the wild type strain increased the levels of many polypeptides in the culture supernatant after the late exponential growth phase. Such polypeptides included both cytoplasmic and secretory proteins, suggesting proteins secreted or released into the medium were degraded by Clp. To assess the effects of Clp on the productivity and stability of recombinant proteins, 74-kDa NanI sialidase was expressed in the two strains. The mutant strain produced a higher level of NanI activity than the wild type strain. Furthermore, under the conditions where Clp was activated, NanI was degraded easily in the latter culture but not in the former one. These results indicate that the Clp⁻ mutant could serve as a useful strain for efficiently expressing and preparing protease-free clostridial proteins.     

Subcellular Localization of the Major Autolysin,ATL and Its Processed Proteins in Staphylococcus aureus

The Staphylococcus aureus autolysin gene, atl, encodes a unique 138-kDa protein (ATL) with amidase and glucosaminidase domains. ATL has been suggested to undergo proteolytic processing to generate two extracellular peptidoglycan hydrolases, 51-kDa endo-β-N-acetylglucosaminidase (51-kDa GL) and 62-kDa N-acetylmuramyl-L-alanine amidase (62-kDa AM). To investigate cell-associated bacteriolytic enzymes for atl gene products, proteins were extracted from the cells as follows. The cells were exposed to 3 M LiCl followed by 4% SDS. Thereafter, the cells were disrupted and again extracted with 4% SDS. Whole SDS-stable cell-associated bacteriolytic proteins were extracted without disrupting the cells. Exposure to 3 M LiCl released major 138-, 115-, 85-, 62- and 51-kDa bacteriolytic proteins, and subsequent 4% SDS extraction released major 138- and 115-kDa bacteriolytic proteins. These bacteriolytic proteins were missing in extracts of atl mutant RUSAL2 (S. aureus RN450 atl:: Tn551). Immunoblotting studies suggest that these are all atl gene products: the 138-kDa protein is an ATL with a cleaved signal sequence; the 115-and 85-kDa proteins are intermediates; and the 51- and 62-kDa proteins are cell-associated 51-kDa GL and 62-kDa AM, respectively. The trypsin susceptibility of these proteins suggests that they are located outside the cell membrane. Differences in extractability and immunoelectron microscopic studies suggest that atl gene products are associated with cells in two different ways, LiCl extractable and non extractable. We suggest that the 138-kDa ATL undergoes processing through intermediate proteins (115- and 85-kDa proteins) to mature as the active cell cluster-dispersing enzymes 51-kDa GL and 62-kDa AM on the cell surface.     

The importance of<Emphasis Type="Italic"> porE</Emphasis> and<Emphasis Type="Italic"> porF</Emphasis> in the anabolic pyruvate oxidoreductase of<Emphasis Type="Italic"> Methanococcus maripaludi</Emphasis>s

The operon of the anabolic pyruvate oxidoreductase (POR) of Methanococcus maripaludis encodes two genes (porEF) whose functions are unknown. Because these genes possess sequence similarity to polyferredoxins, they may be electron carriers to the POR. To elucidate whether the methanococcal POR requires PorEF for activity, a deletion mutant, strain JJ150, lacking porEF was constructed. Compared to the wild-type strain JJ1, the mutant grew more slowly in minimal medium and minimal plus acetate medium, and pyruvate-dependent methanogenesis was inhibited. In contrast, the methyl-viologen-dependent pyruvate-oxidation activity of POR, carbon monoxide dehydrogenase, and hydrogenase activities of the mutant were similar to those of the wild-type. Upon genetic complementation of the mutant with porEF in the methanococcal shuttle vector pMEV2+porEF, growth in minimal medium and pyruvate-dependent methanogenesis were restored to wild-type levels. Complementation with porE alone restored methanogenesis from pyruvate but not growth in minimal medium. Complementation with porF alone partially restored growth but not methanogenesis from pyruvate. Although the specific roles of porE and porF have not been determined, these results suggest that PorEF play important roles in the anabolic POR in vivo even though they are not required for the dye-dependent activity.Abbreviations CODH/ACS Carbon monoxide dehydrogenase/acetyl-CoA synthase - POR Pyruvate oxidoreductase     

Morphogenetic routes of long-term embryogenic callus culture of <Emphasis Type="Italic">Areca catechu</Emphasis>

Early morphogenetic events and repetitive embryogenesis from callus culture of betel nut palm (Areca catechu L.) were studied using scanning electron microscopy. On Murashige and Skoog (MS) medium supplemented with 2 mg dm⁻³ dicamba, callus culture has capacity to form plantlets via somatic embryogenesis and to form secondary embryos for about 4 years. However, various abnormal embryos without differentiation of the leaf sheath and shoot apical meristem were observed, which showed bell-shaped and then cup-shaped or mushroom-shaped structures. These abnormal embryos contained distinctive structures, including a disk-shape interior region, surfaces with grooves and a stalk-like posterior region. During subculture, these abnormal embryos enlarged, became deformed and gradually lose their shape and then converted into nodular, compact embryogenic callus. It was also found that secondary embryos originated from interior surfaces or posterior regions of abnormal embryos, and gave rise to the next cycle of normal and abnormal embryos.     

An obligate methylotrophic, methane-oxidizing Methylomicrobium species from a highly alkaline environment

A new, obligately methylotrophic, methane-oxidizing bacterium, strain AMO 1, was isolated from a mixed sample of sediments from five highly alkaline soda lakes (Kenya). Based on its cell ultrastructure and high activity of the hexulose-6-phosphate synthase, the new isolate belongs to the type I methanotrophs. It differed, however, from the known neutrophilic methanotrophs by the ability to grow and oxidize methane at high pH values. The bacterium grew optimally with methane at pH 9–10. The oxidation of methane, methanol, and formaldehyde was optimal at pH 10, and cells were still active up to pH 11. AMO 1 was able to oxidize ammonia to nitrite at high pH. A maximal production of nitrite from ammonia in batch cultures at pH 10 was observed with 10% of CH₄ in the gas phase when nitrate was present as nitrogen source. Washed cells of AMO 1 oxidized ammonia most actively at pH 10–10.5 in the presence of limiting amounts of methanol or CH₄. The bacterium was also capable of oxidizing organic sulfur compounds at high pH. Washed cells grown with methane exhibited high activity of CS₂ oxidation and low, but detectable, levels of DMS and DMDS oxidation. The GC content of AMO 1 was 50.9 mol%. It showed only weak DNA homology with the previously described alkaliphilic methanotroph "Methylobacter alcaliphilus" strain 20 Z and with the neutrophilic species of the genera Methylobacter and Methylomonas. According to the 16S rRNA gene sequence analysis, strain AMO 1 was most closely related to a neutrophilic methanotroph, Methylomicrobium pelagicum (98.2% sequence similarity), within the gamma-Proteobacteria. Received: July 26, 1999 / Accepted: January 4, 2000     

Mannosylglycerate is essential for osmotic adjustment in Thermus thermophilus strains HB27 and RQ-1

We disrupted the mpgS encoding mannosyl-3-phosphoglycerate synthase (MpgS) of Thermus thermophilus strains HB27 and RQ-1, by homologous recombination, to assess the role of the compatible solute mannosylglycerate (MG) in osmoadaptation of the mutants, to examine their ability to grow in NaCl-containing medium and to identify the intracellular organic solutes. Strain HB27 accumulated only MG when grown in defined medium containing 2% NaCl; mutant HB27M9 did not grow in the same medium containing more than 1% NaCl. When trehalose or MG was added, the mutant was able to grow up to 2% of NaCl and accumulated trehalose or MG, respectively, plus amino acids. T. thermophilus RQ-1 grew in medium containing up to 5% NaCl, accumulated trehalose and lower amounts of MG. Mutant RQ-1M1 lost the ability to grow in medium containing more than 3% NaCl and accumulated trehalose and moderate levels of amino acids. Exogenous MG did not improve the ability of the organism to grow above 3% NaCl, but caused a decrease in the levels of amino acids. Our results show that MG serves as a compatible solute primarily during osmoadaptation at low levels of NaCl while trehalose is primarily involved in osmoadaptation during growth at higher NaCl levels.     

Antitumor Activity of an Alkali Extract of Clostridium saccharoperbutylacetonicum Cells

Bacillus thuringiensis var. israelensis produces 130-kDa proteins which are toxic to mosquito larvae. The ISRH4 gene encoding 1,180 amino acids of the 130-kDa insecticidal protein was fused with lac Z′ on a plasmid, pUC19, and sequentially deleted from the C-terminus to construct a series of deletion mutants. All the deletion mutant genes directed the production of truncated ISRH4 proteins fused with the α-complementing fragment of β-galactosidase in Escherichia coli cells in the presence of isopropyl β-d-thiogalactopyranoside. Analysis of the mosquito larvicidal activity of deletion mutant proteins revealed that the N-terminal 29 amino acids and the C-terminal 485 amino acids could be removed without loss of the activity.     

Zinc Uptake Regulator (<Emphasis Type="Italic">zur</Emphasis>) Gene Involved in Zinc Homeostasis and Virulence of <Emphasis Type="Italic">Xanthomonas oryzae</Emphasis> pv. <Emphasis Type="Italic">oryzae</Emphasis> in Rice

Xanthomonas oryzae pv. oryzae causes bacterial leaf blight, one of the most widespread and destructive bacterial diseases in rice. In order to understand the gene of zinc uptake regulator (zur) involved in virulence of the pathogen in rice, we generated a mutant OSZRM by homologous suicide plasmid integration. The mutant failed to grow in NYGB medium supplemented with Zn²⁺ or Fe³⁺ at a concentration of 500 μM or 6 mM, whereas the wild-type strain grew well at the same conditions. The zur mutant was hypersensitive to hydrogen peroxide and exhibited reduction catalase activity and the production of extracellular polysaccharide (EPS). Interestingly, the mutant showed a reduction in virulence on rice but still kept triggering hypersensitive response (HR) in tobacco. When the mutant was complemented with the zur gene, the response was recovered to wild-type. These results suggested that zur gene is a functional member of the Zur regulator family that controls zinc and iron homeostasis, oxidative stress, and EPS production, which is necessary for virulence in X. oryzae pv. oryzae. Wanfeng Yang and Yan Liu contributed equally to this work