scholarly journals Fe oxidation by a fused cytochrome-porin common to diverse Fe-oxidizing bacteria

2018 ◽  
Author(s):  
Clara S. Chan ◽  
Sean M. McAllister ◽  
Arkadiy Garber ◽  
Beverly J. Hallahan ◽  
Sharon Rozovsky
Keyword(s):  
Outer Membrane ◽  
Phylogenetic Analyses ◽  
Soil Formation ◽  
Biogeochemical Processes ◽  
Formation Water ◽  
Incomplete Knowledge ◽  
Fe Oxidation ◽  
Function Sequence ◽  
Oxidation Mechanisms ◽  
Common Function

SummaryFe oxidation is one of Earth’s major biogeochemical processes, key to weathering, soil formation, water quality, and corrosion. However, our ability to track the contributions of Fe-oxidizing microbes is limited by our relatively incomplete knowledge of microbial Fe oxidation mechanisms, particularly in neutrophilic Fe-oxidizers. The genomes of many Fe-oxidizers encode homologs to an outer-membrane cytochrome (Cyc2) that has been shown to oxidize Fe in two acidophiles. Here, we demonstrate the Fe oxidase function of a heterologously expressed Cyc2 homolog derived from a neutrophilic Fe oxidizer. Phylogenetic analyses show that Cyc2 from neutrophiles cluster together, suggesting a common function. Sequence analysis and modeling reveal the entire Cyc2 family is defined by a unique structure, a fused cytochromeporin, consistent with Fe oxidation on the outer membrane, preventing internal Fe oxide encrustation. Metatranscriptomes from Fe-oxidizing environments show exceptionally high expression of cyc2, supporting its environmental role in Fe oxidation. Together, these results provide evidence that cyc2 encodes Fe oxidases in diverse Fe-oxidizers and therefore can be used to recognize microbial Fe oxidation. The presence of cyc2 in 897 genomes suggests that microbial Fe oxidation may be a widespread metabolism.

Conceptual Approaches to Pedogenesis

2004 ◽  
Author(s):  
Vance T. Holliday
Keyword(s):  
Process Model ◽  
Soil Formation ◽  
Site Formation ◽  
Biogeochemical Processes ◽  
Pedogenic Process ◽  
Soil Geomorphology ◽  
Multiple Process ◽  
The Many ◽  
Soil Forming Processes ◽  
State Factor

To fully appreciate and apply pedologic principals in archaeology, some of the theoretical underpinnings of pedology and especially soil geomorphology must be outlined. Pedologists and soil geomorphologists have attempted to describe, if not model, the processes of soil formation, the factors that drive the processes, and the evolution of soils as landscapes evolve (summarized by Smeck et al., 1983; Johnson and Watson-Stegner, 1987; and Gerrard, 1992, pp. 1–50, 217–220). The task is a difficult one, however, because of the complex and variable sets of processes responsible for soil development. Several of the resulting approaches have proven useful for conceptualizing pedogenesis and, more important, for interpreting soils. In addition to understanding soil-forming processes for interpreting soil profiles, understanding soil formation is important for understanding site formation. The conceptual approaches particularly useful in soil geomorphic and geoarchaeological research are summarized below. Soil-forming processes as components of site formation are discussed more fully in chapter 10. The following discussions of conceptual approaches to pedogenesis are roughly arranged in order of increasing complexity. The “multiple-process model” is essentially a categorization of soil-forming processes. It does not explain pedogenesis but is a useful way to sort and group the many soil-forming processes. The “state factor” approach and the “K-cycle” concept do not deal directly with soil formation, but instead focus on important external factors and processes that drive or affect pedogenesis such as climate and geomorphic evolution. The “soil evolution” model and the “new global view of soils” attempt to integrate pedogenic process with landscape evolution, climate, and other factors. This section closes with discussion of two important aspects of pedogenesis and pedogenic pathways that offer caveats in the use of soils for reconstructing the past. Soils are the result of biogeochemical processes determined and driven by the ecosystem (following Buol et al., 1997). This relationship is more simply described as “internal soil-forming processes” driven by “external soil-forming factors” (fig. 3.1; after Buol et al., 1984). A useful approach to categorizing the many and varied internal soil-forming processes responsible for pedogenesis is the multiple-process model of Simonson (1959, 1978).

Phylogeny of Terrestrial Isopods Based on the Complete Mitochondrial Genomes, Subvert the Monophyly of Oniscidea

2020 ◽  
Author(s):  
Rui Zhang ◽  
Ruru Chen ◽  
Jianmei An ◽  
Carlos A. Santamaria
Keyword(s):  
Phylogenetic Analyses ◽  
Soil Formation ◽  
Taxonomic Status ◽  
Mitochondrial Genomes ◽  
Phylogenetic Hypothesis ◽  
Terrestrial Isopods ◽  
The Family ◽  
Complete Mitochondrial Genomes

Abstract Background: Oniscidea is the only truly terrestrial taxon within the Crustacea, and vital to soil formation. However, the monophyly of suborder Oniscidea has been in dispute since 1995, with different studies disagreeing on whether the coastal Ligiidae are included within the suborder. To clarify the phylogenetic hypothesis of suborder Oniscidea, we sequenced the complete mitochondrial genomes of Ligia exotica (Roux, 1828) and Mongoloniscus sinensis (Dollfus, 1901).Results: Like most metazoan, the complete mitogenomes of two species with circular double strands. The structure and characters of mitogenomes of these two species are analyzed. The constructed phylogenetic analyses show that Oniscidea is polyphyletic group, with Ligia being more closely related to marine isopods (Valvifera + Cymothoida + Sphaeromatidea).Conclusions: We elevate the taxonomic status of the family Ligiidae to the suborder Ligiaidea which are with parallel rank with Oniscidea. Ligiaidea is much primitive than other exact terrestrial isopods. Crinocheta are strongly monophyly, family Agnaridae is more closely related to Porcellionidae rather than Armadillididae.

scholarly journals The ompA Gene in Chlamydia trachomatis Differs in Phylogeny and Rate of Evolution from Other Regions of the Genome

2006 ◽  
Vol 74 (1) ◽  
pp. 578-585 ◽  
Author(s):  
Brian W. Brunelle ◽  
George F. Sensabaugh
Keyword(s):  
Chlamydia Trachomatis ◽  
Membrane Protein ◽  
Outer Membrane ◽  
Outer Membrane Protein ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Housekeeping Genes ◽  
Phylogenetic Characterization ◽  
Tissue Tropisms

ABSTRACT Strains of Chlamydia trachomatis are classified into serovars based on nucleotide sequence differences in ompA, the gene that encodes the major outer membrane protein. Phylogenetic characterization of strains based on ompA, however, results in serovar groupings that are inconsistent with the distinguishing features of C. trachomatis pathobiology, e.g., tissue tropisms and disease presentation. We have compared nucleotide sequences at multiple sites distributed around the chlamydial genome from 18 strains representing 16 serovars; sampled regions included genes encoding housekeeping enzymes (totaling 2,073 bp), intergenic noncoding segments (1,612 bp), and a gene encoding a second outer membrane protein (porB; 1,023 bp), with the ompA sequence (1,194 bp) used for reference. These comparative analyses revealed substantial variation in nucleotide substitution patterns among the sampled regions, with average pairwise sequence differences ranging from 0.15% for the housekeeping genes to 12.1% for ompA. Phylogenetic characterization of the sampled genomic sequences yielded a strongly supported tree that divides the strains into groupings consistent with C. trachomatis biology and which has a topology quite distinct from the ompA tree. This phylogenetic incongruity can be accounted for by recombination of the ompA gene between different genomic backgrounds. We found, however, no evidence of recombination within or between any of the sampled regions around the C. trachomatis genome apart from ompA. Parallel analysis of published sequence data on four members of the pmp gene family are consistent with the phylogenetic analyses reported here.

scholarly journals Pivotal Roles of the Outer Membrane Polysaccharide Export and Polysaccharide Copolymerase Protein Families in Export of Extracellular Polysaccharides in Gram-Negative Bacteria

2009 ◽  
Vol 73 (1) ◽  
pp. 155-177 ◽  
Author(s):  
Leslie Cuthbertson ◽  
Iain L. Mainprize ◽  
James H. Naismith ◽  
Chris Whitfield
Keyword(s):  
Outer Membrane ◽  
Cell Biology ◽  
Pathogenic Bacteria ◽  
Phylogenetic Analyses ◽  
Barrier Properties ◽  
Extracellular Polysaccharides ◽  
Molecular Scaffolds ◽  
Macromolecular Trafficking ◽  
Structural Relationships ◽  
And Function

SUMMARY Many bacteria export extracellular polysaccharides (EPS) and capsular polysaccharides (CPS). These polymers exhibit remarkably diverse structures and play important roles in the biology of free-living, commensal, and pathogenic bacteria. EPS and CPS production represents a major challenge because these high-molecular-weight hydrophilic polymers must be assembled and exported in a process spanning the envelope, without compromising the essential barrier properties of the envelope. Emerging evidence points to the existence of molecular scaffolds that perform these critical polymer-trafficking functions. Two major pathways with different polymer biosynthesis strategies are involved in the assembly of most EPS/CPS: the Wzy-dependent and ATP-binding cassette (ABC) transporter-dependent pathways. They converge in an outer membrane export step mediated by a member of the outer membrane auxiliary (OMA) protein family. OMA proteins form outer membrane efflux channels for the polymers, and here we propose the revised name outer membrane polysaccharide export (OPX) proteins. Proteins in the polysaccharide copolymerase (PCP) family have been implicated in several aspects of polymer biogenesis, but there is unequivocal evidence for some systems that PCP and OPX proteins interact to form a trans-envelope scaffold for polymer export. Understanding of the precise functions of the OPX and PCP proteins has been advanced by recent findings from biochemistry and structural biology approaches and by parallel studies of other macromolecular trafficking events. Phylogenetic analyses reported here also contribute important new insight into the distribution, structural relationships, and function of the OPX and PCP proteins. This review is intended as an update on progress in this important area of microbial cell biology.

Molecular Structure of the Outermost Cell Wall Component of Spirillum Serpens

1977 ◽  
Vol 35 ◽  
pp. 342-343
Author(s):  
Wah Chiu ◽  
David Grano
Keyword(s):  
Molecular Structure ◽  
Cell Wall ◽  
Outer Membrane ◽  
Gel Electrophoresis ◽  
Electron Microscopic Examination ◽  
Electron Microscopic ◽  
Cell Wall Component ◽  
Protein Components ◽  
Exposure Technique ◽  
Structural Aspects

The periodic structure external to the outer membrane of Spirillum serpens VHA has been isolated by similar procedures to those used by Buckmire and Murray (1). From SDS gel electrophoresis, we have found that the isolated fragments contain several protein components, and that the crystalline structure is composed of a glycoprotein component with a molecular weight of ∽ 140,000 daltons (2). Under an electron microscopic examination, we have visualized the hexagonally-packed glycoprotein subunits, as well as the bilayer profile of the outer membrane. In this paper, we will discuss some structural aspects of the crystalline glycoproteins, based on computer-reconstructed images of the external cell wall fragments.The specimens were prepared for electron microscopy in two ways: negatively stained with 1% PTA, and maintained in a frozen-hydrated state (3). The micrographs were taken with a JEM-100B electron microscope with a field emission gun. The minimum exposure technique was essential for imaging the frozen- hydrated specimens.

Cryo-Electron Microscopy and Correlation Averaging of Frozen-Hydrated, Polymorphic 2D Crystals of the Mitochondrial Outer Membrane Channel

1990 ◽  
Vol 48 (1) ◽  
pp. 100-101
Author(s):  
Xiao-Wei Guo
Keyword(s):  
Outer Membrane ◽  
Hexagonal Lattice ◽  
Mitochondrial Outer Membrane ◽  
Rectangular Lattice ◽  
Electron Microscopic ◽  
Cryo Electron Microscopy ◽  
Voltage Dependent ◽  
Outer Membrane Channel ◽  
2D Crystals ◽  
Vdac Channel

Voltage-dependent, anion-selective channels (VDAC) are formed in the mitochondrial outer membrane (mitOM) by a 30-kDa polypeptide. These channels form ordered 2D arrays when mitOMs from Neurospora crassa are treated with soluble phospholipase A2. We obtain low-dose electron microscopic images of unstained specimens of VDAC crystals preserved in vitreous ice, using a Philips EM420 equipped with a Gatan cryo-transfer stage. We then use correlation analysis to compute average projections of the channel crystals. The procedure involves Fourier-filtration of a region within a crystal field to obtain a preliminary average that is subsequently cross-correlated with the entire crystal. Subregions are windowed from the crystal image at coordinates of peaks in the cross-correlation function (CCF, see Figures 1 and 2) and summed to form averages (Figure 3).The VDAC channel forms several different types of crystalline arrays in mitOMs. The polymorph first observed during phospholipase treatment is a parallelogram array (a=13 run, b=11.5 run, θ==109°) containing 6 water-filled pores per unit cell. Figure 1 shows the CCF of a sub-field of such an “oblique” array used to compute the correlation average of Figure 3A. With increased phospholipase treatment, other polymorphs are observed, often co-existing within the same crystal. For example, two distinct (but closely related) types of lattices occur in the field corresponding to the CCF of Figure 2: a “contracted” version of the parallelogram lattice (a=13 run, b=10 run, θ=99°), and a near-rectangular lattice (a=8.5 run, b=5 nm). The pattern of maxima in this CCF suggests that a third, near-hexagonal lattice (a=4.5 nm) may also be present. The correlation averages of Figures 3B-D were computed from polycrystalline fields, using peak coordinates in regions of CCFs corresponding to each of the three lattice types.

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