NifH and NifD phylogenies: an evolutionary basis for understanding nitrogen fixation capabilities of methanotrophic bacteria

Microbiology ◽  
2004 ◽  
Vol 150 (5) ◽  
pp. 1301-1313 ◽  
Author(s):  
Svetlana N. Dedysh ◽  
Peter Ricke ◽  
Werner Liesack
Keyword(s):  
16S Rrna ◽  
Amino Acid Sequences ◽  
Phenotypic Trait ◽  
Type I ◽  
Methanotrophic Bacteria ◽  
Type Ii ◽  
Methylococcus Capsulatus ◽  
Available Nitrogen ◽  
Active Growth ◽  
Nitrogen Acquisition

The ability to utilize dinitrogen as a nitrogen source is an important phenotypic trait in most currently known methanotrophic bacteria (MB). This trait is especially important for acidophilic MB, which inhabit acidic oligotrophic environments, highly depleted in available nitrogen compounds. Phylogenetically, acidophilic MB are most closely related to heterotrophic dinitrogen-fixing bacteria of the genus Beijerinckia. To further explore the phylogenetic linkage between these metabolically different organisms, the sequences of nifH and nifD gene fragments from acidophilic MB of the genera Methylocella and Methylocapsa, and from representatives of Beijerinckia, were determined. For reference, nifH and nifD sequences were also obtained from some type II MB of the alphaproteobacterial Methylosinus/Methylocystis group and from gammaproteobacterial type I MB. The trees constructed for the inferred amino acid sequences of nifH and nifD were highly congruent. The phylogenetic relationships among MB in the NifH and NifD trees also agreed well with the corresponding 16S rRNA-based phylogeny, except for two distinctive features. First, different methods used for phylogenetic analysis grouped the NifH and NifD sequences of strains of the gammaproteobacterial MB Methylococcus capsulatus within a clade mainly characterized by Alphaproteobacteria, including acidophilic MB and type II MB of the Methylosinus/Methylocystis group. From this and other genomic data from Methylococcus capsulatus Bath, it is proposed that an ancient event of lateral gene transfer was responsible for this aberrant branching. Second, the identity values of NifH and NifD sequences between Methylocapsa acidiphila B2 and representatives of Beijerinckia were clearly higher (98·5 and 96·6 %, respectively) than would be expected from their 16S rRNA-based relationships. Possibly, these two bacteria originated from a common acidophilic dinitrogen-fixing ancestor, and were subject to similar evolutionary pressure with regard to nitrogen acquisition. This interpretation is corroborated by the observation that, in contrast to most other diazotrophs, M. acidiphila B2 and Beijerinckia spp. are capable of active growth on nitrogen-free media under fully aerobic conditions.

scholarly journals Effect of Afforestation and Reforestation of Pastures on the Activity and Population Dynamics of Methanotrophic Bacteria

2007 ◽  
Vol 73 (16) ◽  
pp. 5153-5161 ◽  
Author(s):  
Brajesh K. Singh ◽  
Kevin R. Tate ◽  
Gokul Kolipaka ◽  
Carolyn B. Hedley ◽  
Catriona A. Macdonald ◽  
...  
Keyword(s):  
Community Structure ◽  
Methane Oxidation ◽  
Phospholipid Fatty Acid ◽  
Pine Forest ◽  
Polymorphism Analysis ◽  
Type I ◽  
Methanotrophic Bacteria ◽  
Type Ii ◽  
Methylococcus Capsulatus ◽  
Methanotrophic Communities

ABSTRACT We investigated the effect of afforestation and reforestation of pastures on methane oxidation and the methanotrophic communities in soils from three different New Zealand sites. Methane oxidation was measured in soils from two pine (Pinus radiata) forests and one shrubland (mainly Kunzea ericoides var. ericoides) and three adjacent permanent pastures. The methane oxidation rate was consistently higher in the pine forest or shrubland soils than in the adjacent pasture soils. A combination of phospholipid fatty acid (PLFA) and stable isotope probing (SIP) analyses of these soils revealed that different methanotrophic communities were active in soils under the different vegetations. The C18 PLFAs (signature of type II methanotrophs) predominated under pine and shrublands, and C16 PLFAs (type I methanotrophs) predominated under pastures. Analysis of the methanotrophs by molecular methods revealed further differences in methanotrophic community structure under the different vegetation types. Cloning and sequencing and terminal-restriction fragment length polymorphism analysis of the particulate methane oxygenase gene (pmoA) from different samples confirmed the PLFA-SIP results that methanotrophic bacteria related to type II methanotrophs were dominant in pine forest and shrubland, and type I methanotrophs (related to Methylococcus capsulatus) were dominant in all pasture soils. We report that afforestation and reforestation of pastures caused changes in methane oxidation by altering the community structure of methanotrophic bacteria in these soils.

scholarly journals Differential detection of type II methanotrophic bacteria in acidic peatlands using newly developed 16S rRNA-targeted fluorescent oligonucleotide probes

2003 ◽  
Vol 43 (3) ◽  
pp. 299-308 ◽  
Author(s):  
Svetlana N Dedysh ◽  
Peter F Dunfield ◽  
Manigee Derakshani ◽  
Stephan Stubner ◽  
Jürgen Heyer ◽  
...  
Keyword(s):  
16S Rrna ◽  
Differential Detection ◽  
Methanotrophic Bacteria ◽  
Oligonucleotide Probes ◽  
Type Ii

scholarly journals Family- and Genus-Level 16S rRNA-Targeted Oligonucleotide Probes for Ecological Studies of Methanotrophic Bacteria

2001 ◽  
Vol 67 (10) ◽  
pp. 4726-4733 ◽  
Author(s):  
Jay Gulledge ◽  
Azeem Ahmad ◽  
Paul A. Steudler ◽  
William J. Pomerantz ◽  
Colleen M. Cavanaugh
Keyword(s):  
16S Rrna ◽  
Environmental Samples ◽  
Quantitative Information ◽  
Negative Control ◽  
Type I ◽  
Methanotrophic Bacteria ◽  
Oligonucleotide Probes ◽  
Ecological Studies ◽  
Dot Blot ◽  
The Family

ABSTRACT Methanotrophic bacteria play a major role in the global carbon cycle, degrade xenobiotic pollutants, and have the potential for a variety of biotechnological applications. To facilitate ecological studies of these important organisms, we developed a suite of oligonucleotide probes for quantitative analysis of methanotroph-specific 16S rRNA from environmental samples. Two probes target methanotrophs in the family Methylocystaceae(type II methanotrophs) as a group. No oligonucleotide signatures that distinguish between the two genera in this family,Methylocystis and Methylosinus, were identified. Two other probes target, as a single group, a majority of the known methanotrophs belonging to the familyMethylococcaceae (type I/X methanotrophs). The remaining probes target members of individual genera of theMethylococcaceae, includingMethylobacter, Methylomonas,Methylomicrobium, Methylococcus, andMethylocaldum. One of the family-level probes also covers all methanotrophic endosymbionts of marine mollusks for which 16S rRNA sequences have been published. The two known species of the newly described genus Methylosarcina gen. nov. are covered by a probe that otherwise targets only members of the closely related genus Methylomicrobium. None of the probes covers strains of the newly proposed generaMethylocella and “Methylothermus,” which are polyphyletic with respect to the recognized methanotrophic families. Empirically determined midpoint dissociation temperatures were 49 to 57°C for all probes. In dot blot screening against RNA from positive- and negative-control strains, the probes were specific to their intended targets. The broad coverage and high degree of specificity of this new suite of probes will provide more detailed, quantitative information about the community structure of methanotrophs in environmental samples than was previously available.

scholarly journals The lspA Gene, Encoding the Type II Signal Peptidase of Rickettsia typhi: Transcriptional and Functional Analysis

2006 ◽  
Vol 189 (2) ◽  
pp. 336-341 ◽  
Author(s):  
M. Sayeedur Rahman ◽  
Shane M. Ceraul ◽  
Sheila M. Dreher-Lesnick ◽  
Magda S. Beier ◽  
Abdu F. Azad
Keyword(s):  
Amino Acid Sequences ◽  
Signal Peptidase ◽  
Secretory Proteins ◽  
Transcriptional Level ◽  
Temperature Sensitive ◽  
Type I ◽  
Type Ii ◽  
Intracellular Growth ◽  
Rickettsia Typhi ◽  
Differential Expression Pattern

ABSTRACT Lipoprotein processing by the type II signal peptidase (SPase II) is known to be critical for intracellular growth and virulence for many bacteria, but its role in rickettsiae is unknown. Here, we describe the analysis of lspA, encoding a putative SPase II, an essential component of lipoprotein processing in gram-negative bacteria, from Rickettsia typhi. Alignment of deduced amino acid sequences shows the presence of highly conserved residues and domains that are essential for SPase II activity in lipoprotein processing. The transcription of lspA, lgt (encoding prolipoprotein transferase), and lepB (encoding type I signal peptidase), monitored by real-time quantitative reverse transcription-PCR, reveals a differential expression pattern during various stages of rickettsial intracellular growth. The higher transcriptional level of all three genes at the preinfection time point indicates that only live and metabolically active rickettsiae are capable of infection and inducing host cell phagocytosis. lspA and lgt, which are involved in lipoprotein processing, show similar levels of expression. However, lepB, which is involved in nonlipoprotein secretion, shows a higher level of expression, suggesting that LepB is the major signal peptidase for protein secretion and supporting our in silico prediction that out of 89 secretory proteins, only 14 are lipoproteins. Overexpression of R. typhi lspA in Escherichia coli confers increased globomycin resistance, indicating its function as SPase II. In genetic complementation, recombinant lspA from R. typhi significantly restores the growth of temperature-sensitive E. coli Y815 at the nonpermissive temperature, supporting its biological activity as SPase II in prolipoprotein processing.

scholarly journals Amino acid sequences of α-helical segments from S-carboxymethylkerateine-A. Complete sequence of a type-II segment

1978 ◽  
Vol 173 (2) ◽  
pp. 365-371 ◽  
Author(s):  
W G Crewther ◽  
A S Inglis ◽  
N M McKern
Keyword(s):  
Amino Acid ◽  
Coiled Coil ◽  
Complete Sequence ◽  
Amino Acid Sequences ◽  
Helical Axis ◽  
Type I ◽  
Type Ii ◽  
Coil Structure ◽  
Aqueous Urea ◽  
Alpha Keratin

1. The helical fragments obtained by partial chymotryptic digestion of S-carboxymethylkeratine-A, the low-sulphur fraction from wool, were fractionated into type-I and type-II helical segments in aqueous urea under conditions limiting carbamoylation. 2. The amino acid sequence of a 109-residue type-II segment was completed by using the sequenator. 3. When the data were incorporated into a helical model of 3.6 residues per turn the hydrophobic residues generated a band aligned at a slight angle to the helical axis. This result is in accord with the postulated coiled-coil structure of the crystalline regions of alpha-keratin.

scholarly journals Methanotroph Diversity in Landfill Soil: Isolation of Novel Type I and Type II Methanotrophs Whose Presence Was Suggested by Culture-Independent 16S Ribosomal DNA Analysis

1999 ◽  
Vol 65 (11) ◽  
pp. 4887-4897 ◽  
Author(s):  
Mark G. Wise ◽  
J Vaun McArthur ◽  
Lawrence J. Shimkets
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Ribosomal Dna ◽  
Rrna Gene ◽  
Type I ◽  
Type Ii ◽  
Partial Sequencing ◽  
16S Ribosomal Dna ◽  
Culture Independent ◽  
The 16S Rrna Gene

ABSTRACT The diversity of the methanotrophic community in mildly acidic landfill cover soil was assessed by three methods: two culture-independent molecular approaches and a traditional culture-based approach. For the first of the molecular studies, two primer pairs specific for the 16S rRNA gene of validly published type I (including the former type X) and type II methanotrophs were identified and tested. These primers were used to amplify directly extracted soil DNA, and the products were used to construct type I and type II clone libraries. The second molecular approach, based on denaturing gradient gel electrophoresis (DGGE), provided profiles of the methanotrophic community members as distinguished by sequence differences in variable region 3 of the 16S ribosomal DNA. For the culturing studies, an extinction-dilution technique was employed to isolate slow-growing but numerically dominant strains. The key variables of the series of enrichment conditions were initial pH (4.8 versus 6.8), air/CH4/CO2 headspace ratio (50:45:5 versus 90:9:1), and concentration of the medium (1× nitrate minimal salts [NMS] versus 0.2× NMS). Screening of the isolates showed that the nutrient-rich 1× NMS selected for type I methanotrophs, while the nutrient-poor 0.2× NMS tended to enrich for type II methanotrophs. Partial sequencing of the 16S rRNA gene from selected clones and isolates revealed some of the same novel sequence types. Phylogenetic analysis of the type I clone library suggested the presence of a new phylotype related to the Methylobacter-Methylomicrobiumgroup, and this was confirmed by isolating two members of this cluster. The type II clone library also suggested the existence of a novel group of related species distinct from the validly publishedMethylosinus and Methylocystis genera, and two members of this cluster were also successfully cultured. Partial sequencing of the pmoA gene, which codes for the 27-kDa polypeptide of the particulate methane monooxygenase, reaffirmed the phylogenetic placement of the four isolates. Finally, not all of the bands separated by DGGE could be accounted for by the clones and isolates. This polyphasic assessment of community structure demonstrates that much diversity among the obligate methane oxidizers has yet to be formally described.

Sequence and expression of a type II keratin, K5, in human epidermal cells

1988 ◽  
Vol 8 (1) ◽  
pp. 486-493
Author(s):  
R Lersch ◽  
E Fuchs
Keyword(s):  
Human Gene ◽  
Basal Layer ◽  
Epidermal Cells ◽  
Amino Acid Sequences ◽  
Type I ◽  
Type Ii ◽  
Gene Encoding ◽  
Human Epidermal Cells ◽  
Rna Blot Analysis

We report here the cDNA and amino acid sequences of a human 58-kilodalton type II keratin, K5, which is coexpressed with a 50-kilodalton type I keratin partner, K14, in stratified squamous epithelia. Using a probe specific for the 3'-noncoding portion of this K5 cDNA, we demonstrated the existence of a single human gene encoding this sequence. Using Northern (RNA) blot analysis and in situ hybridization with cRNA probes for both K5 and K14, we examined the expression of these mRNAs in the epidermis and in cultured epidermal cells. Our results indicate that the mRNAs for K5 and K14 are coordinately expressed and abundant in the basal layer of the epidermis. As cells undergo a commitment to terminally differentiate, the expression of both mRNAs seems to be downregulated.

Methylohalobius crimeensis gen. nov., sp. nov., a moderately halophilic, methanotrophic bacterium isolated from hypersaline lakes of Crimea

2005 ◽  
Vol 55 (5) ◽  
pp. 1817-1826 ◽  
Author(s):  
Jürgen Heyer ◽  
Ursula Berger ◽  
Martin Hardt ◽  
Peter F. Dunfield
Keyword(s):  
Fatty Acids ◽  
16S Rrna ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Type I ◽  
Methanotrophic Bacteria ◽  
Rrna Gene Sequence ◽  
Methanotrophic Bacterium ◽  
Hypersaline Lakes ◽  
Novel Genus And Species

A novel genus and species are proposed for two strains of methanotrophic bacteria isolated from hypersaline lakes in the Crimean Peninsula of Ukraine. Strains 10KiT and 4Kr are moderate halophiles that grow optimally at 1–1·5 M (5·8–8·7 %, w/v) NaCl and tolerate NaCl concentrations from 0·2 M up to 2·5 M (1·2–15 %). This optimum and upper limit are the highest for any methanotrophic bacterium known to date. The strains are Gram-negative, aerobic, non-pigmented, motile, coccoid to spindle-shaped bacteria that grow on methane or methanol only and utilize the ribulose monophosphate pathway for carbon assimilation. They are neutrophilic (growth occurs only in the range pH 6·5–7·5) and mesophilic (optimum growth occurs at 30 °C). On the basis of 16S rRNA gene sequence phylogeny, strains 10KiT and 4Kr represent a type I methanotroph within the ‘Gammaproteobacteria’. However, the 16S rRNA gene sequence displays <91·5 % identity to any public-domain sequence. The most closely related methanotrophic bacterium is the thermophilic strain HB. The DNA G+C content is 58·7 mol%. The major phospholipid fatty acids are 18 : 1ω7 (52–61 %), 16 : 0 (22–23 %) and 16 : 1ω7 (14–20 %). The dominance of 18 : 1 over 16 : 0 and 16 : 1 fatty acids is unique among known type I methanotrophs. The data suggest that strains 10KiT and 4Kr should be considered as belonging to a novel genus and species of type I methanotrophic bacteria, for which the name Methylohalobius crimeensis gen. nov., sp. nov. is proposed. Strain 10KiT (=DSM 16011T=ATCC BAA-967T) is the type strain.

scholarly journals Amino acid sequences of α-helical segments from S-carbosymethylkerateine-A. Complete sequence of a type-I segment

1978 ◽  
Vol 173 (2) ◽  
pp. 373-385 ◽  
Author(s):  
K H Gough ◽  
A S Inglis ◽  
W G Crewther
Keyword(s):  
Amino Acid ◽  
Sequence Data ◽  
Coiled Coil ◽  
Alpha Helix ◽  
Protein S ◽  
Amino Acid Sequences ◽  
Type I ◽  
Type Ii ◽  
Sequencing Data ◽  
Helical Segment

The amino acid sequence of a type-I helical segment from the low-sulphur protein (S-carboxymethylkerateine-A) of wool was determined by combining automatic and manual-sequencing data. Whereas in the type-II helical segment most of the cationic groups occur in pairs, 11 of the 22 anionic residues in the sequence of the type-I segment were situated next to a second anionic residue. This suggests possible interactions between type-I and type-II helical segments in alpha-keratin. As observed with the sequence of a type-II helical segment a model constructed on 3.6 residues per turn of helix shows a line of hydrophobic residues along the helix, thereby supporting the physicochemical evidence that the molecule is predominantly helical and forms part of a coiled-coil structure. Examination of the sequence data by predictive methods indicates the possibilty of extensive sections of alpha-helix interspersed with discontinuities. The molecule contains a number of regions with peptide sequences identical with those found by other workers after enzymic digestion of fractions from oxidized wool.

scholarly journals Sequence and expression of a type II keratin, K5, in human epidermal cells.

1988 ◽  
Vol 8 (1) ◽  
pp. 486-493 ◽  
Author(s):  
R Lersch ◽  
E Fuchs
Keyword(s):  
Human Gene ◽  
Basal Layer ◽  
Epidermal Cells ◽  
Amino Acid Sequences ◽  
Type I ◽  
Type Ii ◽  
Gene Encoding ◽  
Human Epidermal Cells ◽  
Rna Blot Analysis

We report here the cDNA and amino acid sequences of a human 58-kilodalton type II keratin, K5, which is coexpressed with a 50-kilodalton type I keratin partner, K14, in stratified squamous epithelia. Using a probe specific for the 3'-noncoding portion of this K5 cDNA, we demonstrated the existence of a single human gene encoding this sequence. Using Northern (RNA) blot analysis and in situ hybridization with cRNA probes for both K5 and K14, we examined the expression of these mRNAs in the epidermis and in cultured epidermal cells. Our results indicate that the mRNAs for K5 and K14 are coordinately expressed and abundant in the basal layer of the epidermis. As cells undergo a commitment to terminally differentiate, the expression of both mRNAs seems to be downregulated.

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