''Gemmata obscuriglobus'' is a species of
Gram-negative
Gram-negative bacteria are bacteria that do not retain the crystal violet stain used in the Gram staining method of bacterial differentiation. They are characterized by their cell envelopes, which are composed of a thin peptidoglycan cell wall ...
,
aerobic
Aerobic means "requiring air," in which "air" usually means oxygen.
Aerobic may also refer to
* Aerobic exercise, prolonged exercise of moderate intensity
* Aerobics, a form of aerobic exercise
* Aerobic respiration, the aerobic process of cel ...
,
heterotrophic
A heterotroph (; ) is an organism that cannot produce its own food, instead taking nutrition from other sources of organic carbon, mainly plant or animal matter. In the food chain, heterotrophs are primary, secondary and tertiary consumers, but ...
bacteria
Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among ...
of the
phylum
In biology, a phylum (; plural: phyla) is a level of classification or taxonomic rank below kingdom and above class. Traditionally, in botany the term division has been used instead of phylum, although the International Code of Nomenclature f ...
Planctomycetota
The Planctomycetota are a phylum of widely distributed bacteria, occurring in both aquatic and terrestrial habitats. They play a considerable role in global carbon and nitrogen cycles, with many species of this phylum capable of anaerobic ammoniu ...
. ''G. obscuriglobus'' occur in freshwater habitats
and was first described in 1984,
and is the only described species in its genus.
''G. obscuriglobus'' is exceptional for its unusual
morphology
Morphology, from the Greek and meaning "study of shape", may refer to:
Disciplines
* Morphology (archaeology), study of the shapes or forms of artifacts
* Morphology (astronomy), study of the shape of astronomical objects such as nebulae, galaxies ...
and for the unusual features in its
genome
In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding ge ...
, often considered to represent large differences in internal organization compared with most
prokaryote
A prokaryote () is a single-celled organism that lacks a nucleus and other membrane-bound organelles. The word ''prokaryote'' comes from the Greek πρό (, 'before') and κάρυον (, 'nut' or 'kernel').Campbell, N. "Biology:Concepts & Connec ...
s
Structure and Morphology
Cell shape and appendages
''G. obscuriglobus'' is a large, roughly spherical bacterium with a cell diameter of 1–2
μm. It is motile and possesses multiple
flagella
A flagellum (; ) is a hairlike appendage that protrudes from certain plant and animal sperm cells, and from a wide range of microorganisms to provide motility. Many protists with flagella are termed as flagellates.
A microorganism may have f ...
per cell.
Internal cell composition
Dense, compact DNA and a deeply invaginated membrane are characteristics of the species.
Membrane structure
Among the most notable features of ''G. obscuriglobus'' is its highly complex and morphologically distinctive
cell membrane
The cell membrane (also known as the plasma membrane (PM) or cytoplasmic membrane, and historically referred to as the plasmalemma) is a biological membrane that separates and protects the interior of all cells from the outside environment ( ...
system, including deep invaginations of its membrane that historically have been described as closed internal membranes that may surround the bacterium's
DNA by analogy to a
eukaryotic
Eukaryotes () are organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the three domains of life. Bacte ...
cell nucleus
The cell nucleus (pl. nuclei; from Latin or , meaning ''kernel'' or ''seed'') is a membrane-bound organelle found in eukaryotic cells. Eukaryotic cells usually have a single nucleus, but a few cell types, such as mammalian red blood cells, h ...
.
The concept of membrane-bound genetic material has been described as a "cell plan" unique to a proposed PVC
superphylum composed of the
Planctomycetota
The Planctomycetota are a phylum of widely distributed bacteria, occurring in both aquatic and terrestrial habitats. They play a considerable role in global carbon and nitrogen cycles, with many species of this phylum capable of anaerobic ammoniu ...
,
Verrucomicrobiota
Verrucomicrobiota is a phylum of Gram-negative bacteria that contains only a few described species. The species identified have been isolated from fresh water, marine and soil environments and human faeces. A number of as-yet uncultivated speci ...
, and
Chlamydiota and distinct from the rest of the
Gram-negative
Gram-negative bacteria are bacteria that do not retain the crystal violet stain used in the Gram staining method of bacterial differentiation. They are characterized by their cell envelopes, which are composed of a thin peptidoglycan cell wall ...
bacteria. The question of whether ''G. obscuriglobus'' and other members of the PVC group possess closed internal membranes and therefore have a unique "cell plan" is considered important in understanding the
evolution
Evolution is change in the heritable characteristics of biological populations over successive generations. These characteristics are the expressions of genes, which are passed on from parent to offspring during reproduction. Variation ...
of membrane-bound compartments, which are often considered a distinguishing feature between
eukaryote
Eukaryotes () are organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the three domains of life. Bacte ...
s and
prokaryote
A prokaryote () is a single-celled organism that lacks a nucleus and other membrane-bound organelles. The word ''prokaryote'' comes from the Greek πρό (, 'before') and κάρυον (, 'nut' or 'kernel').Campbell, N. "Biology:Concepts & Connec ...
s; the lineage that gave rise to the PVC superphylum is speculated to be related to an "intermediate" state between prokaryotes and eukaryotes. The question of how the PVC superfamily membranes are organized and how they relate to eukaryotes is an active and controversial area of research.
Three-dimensional
tomogram
Tomography is imaging by sections or sectioning that uses any kind of penetrating wave. The method is used in radiology, archaeology, biology, atmospheric science, geophysics, oceanography, plasma physics, materials science, astrophysics, quantu ...
reconstructions of whole cells reported in 2013 suggest that contrary to historical belief, ''G. obscuriglobus'' membranes are continuous and do not enclose distinct cellular compartments.
However, this study has been criticized for not detecting or modeling some commonly reported structural features,
and a 2014 study using similar methodology was interpreted as supporting the earlier hypothesis of closed internal compartments.
Membrane and cell wall composition
Early characterization of ''G. obscuriglobus'' found that it lacked a traditional Gram-negative
peptidoglycan
Peptidoglycan or murein is a unique large macromolecule, a polysaccharide, consisting of sugars and amino acids that forms a mesh-like peptidoglycan layer outside the plasma membrane, the rigid cell wall (murein sacculus) characteristic of most ...
(PG)
cell wall
A cell wall is a structural layer surrounding some types of cells, just outside the cell membrane. It can be tough, flexible, and sometimes rigid. It provides the cell with both structural support and protection, and also acts as a filtering mech ...
and instead possessed a proteinaceous exterior layer,
later described as possibly analogous to an
archaea
Archaea ( ; singular archaeon ) is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaebac ...
l
S-layer An S-layer (surface layer) is a part of the cell envelope found in almost all archaea, as well as in many types of bacteria.
The S-layers of both archaea and bacteria consists of a monomolecular layer composed of only one (or, in a few cases, two) ...
.
More recent reports have found the exterior to more closely chemically resemble typical Gram-negative features. Compositional analysis of the membrane has been reported to find
lipopolysaccharide
Lipopolysaccharides (LPS) are large molecules consisting of a lipid and a polysaccharide that are bacterial toxins. They are composed of an O-antigen, an outer core, and an inner core all joined by a covalent bond, and are found in the outer m ...
in ''G. obscuriglobus'', consistent with typical features of Gram-negative
outer membranes.
A 2015 study of several Planctomycetota including ''G. obscuriglobus'' identified the presence of a PG cell wall following the typical Gram-negative structure by both
biochemical
Biochemistry or biological chemistry is the study of chemical processes within and relating to living organisms. A sub-discipline of both chemistry and biology, biochemistry may be divided into three fields: structural biology, enzymology an ...
and
bioinformatic
Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combine ...
analysis.
Reproduction
![Lee bmccellbio 2009 gemmata obscuriglobus budding fig4D](https://upload.wikimedia.org/wikipedia/commons/1/11/Lee_bmccellbio_2009_gemmata_obscuriglobus_budding_fig4D.png)
Like most Planctomycetota, ''G. obscuriglobus'' reproduces by
budding
Budding or blastogenesis is a type of asexual reproduction in which a new organism develops from an outgrowth or bud due to cell division at one particular site. For example, the small bulb-like projection coming out from the yeast cell is know ...
rather than the
fission more commonly observed in bacterial species. It is relatively slow-growing, with an estimated
generation time
In population biology and demography, generation time is the average time between two consecutive generations in the lineages of a population. In human populations, generation time typically ranges from 22 to 33 years. Historians sometimes use this ...
of around 13 hours based on bulk
cell culture
Cell culture or tissue culture is the process by which cells are grown under controlled conditions, generally outside of their natural environment. The term "tissue culture" was coined by American pathologist Montrose Thomas Burrows. This te ...
.
Its life cycle consists of a motile or "swarmer" phase and a
sessile
Sessility, or sessile, may refer to:
* Sessility (motility), organisms which are not able to move about
* Sessility (botany), flowers or leaves that grow directly from the stem or peduncle of a plant
* Sessility (medicine), tumors and polyps that ...
phase during which budding occurs, although these are less distinct than in other Planctomycetota whose life cycles have been studied. Observations of individual cells in culture found that approximately 12 hours were required for bud maturation and separation, followed by an asymmetrical
lag phase
250px, Growth is shown as ''L'' = log(numbers) where numbers is the number of colony forming units per ml, versus ''T'' (time.)
Bacterial growth is proliferation of bacterium into two daughter cells, in a process called binary fission. Providing ...
in which mother cells were quicker to begin a new budding cycle than were newly budded daughter cells.
It has been reported that the budding process involves transfer of naked DNA to the daughter cell, after which it is then surrounded by a nucleoid membrane.
However, three-dimensional reconstructions indicate that DNA is never surrounded by a closed membrane in a newly created bud, but instead is free to diffuse from the mother to daughter cell
cytoplasm
In cell biology, the cytoplasm is all of the material within a eukaryotic cell, enclosed by the cell membrane, except for the cell nucleus. The material inside the nucleus and contained within the nuclear membrane is termed the nucleoplasm. The ...
after the "neck" between the mother and daughter cell membranes, initially as narrow as 30
nanometer
330px, Different lengths as in respect to the molecular scale.
The nanometre (international spelling as used by the International Bureau of Weights and Measures; SI symbol: nm) or nanometer (American and British English spelling differences#-re ...
s, widens sufficiently to accommodate condensed DNA.
Genetic Characterisitcs
Genomic content and organization
The ''G. obscuriglobus''
genome
In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding ge ...
was sequenced by the
J. Craig Venter Institute. The bacterium has a large
genome
In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding ge ...
by the standards of other PVC bacteria, around 9
megabase
A base pair (bp) is a fundamental unit of double-stranded nucleic acids consisting of two nucleobases bound to each other by hydrogen bonds. They form the building blocks of the DNA double helix and contribute to the folded structure of both D ...
s, and contains about 8,000
gene
In biology, the word gene (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a ba ...
s. It has 67%
GC content
In molecular biology and genetics, GC-content (or guanine-cytosine content) is the percentage of nitrogenous bases in a DNA or RNA molecule that are either guanine (G) or cytosine (C). This measure indicates the proportion of G and C bases out ...
. It possesses unusual genetic infrastructure, lacking a key component of most bacterial cell division processes, the protein
FtsZ
FtsZ is a protein encoded by the ''ftsZ'' gene that assembles into a ring at the future site of bacterial cell division (also called the Z ring). FtsZ is a prokaryotic homologue of the eukaryotic protein tubulin. The initials FtsZ mean "Filamen ...
.
A study of
indel
Indel is a molecular biology term for an insertion or deletion of bases in the genome of an organism. It is classified among small genetic variations, measuring from 1 to 10 000 base pairs in length, including insertion and deletion events that ...
s in protein-coding genes of the PVC grouping identified a number of biochemical pathways with unusually high numbers of indels in the ''G. obscuriglobus'' genome, including
ribosomal protein
A ribosomal protein (r-protein or rProtein) is any of the proteins that, in conjunction with rRNA, make up the ribosomal subunits involved in the cellular process of translation. ''E. coli'', other bacteria and Archaea have a 30S small subunit an ...
s.
Nucleoids
One or more nucleoid-like regions of densely compact DNA is commonly observed in ''G. obscuriglobus'' cells. Complex internal structure resembling a
liquid crystal
Liquid crystal (LC) is a state of matter whose properties are between those of conventional liquids and those of solid crystals. For example, a liquid crystal may flow like a liquid, but its molecules may be oriented in a crystal-like way. T ...
has been reported, with some structural similarities to the
chromatin
Chromatin is a complex of DNA and protein found in eukaryotic cells. The primary function is to package long DNA molecules into more compact, denser structures. This prevents the strands from becoming tangled and also plays important roles in r ...
of eukaryotes such as
dinoflagellate
The dinoflagellates (Greek δῖνος ''dinos'' "whirling" and Latin ''flagellum'' "whip, scourge") are a monophyletic group of single-celled eukaryotes constituting the phylum Dinoflagellata and are usually considered algae. Dinoflagellates are ...
s.
The structure of the nucleoid has been implicated in the unusual
radiation
In physics, radiation is the emission or transmission of energy in the form of waves or particles through space or through a material medium. This includes:
* ''electromagnetic radiation'', such as radio waves, microwaves, infrared, visi ...
tolerance of ''G. obscuriglobus''.
Transcription
Transcription refers to the process of converting sounds (voice, music etc.) into letters or musical notes, or producing a copy of something in another medium, including:
Genetics
* Transcription (biology), the copying of DNA into RNA, the fir ...
and
translation
Translation is the communication of the Meaning (linguistic), meaning of a #Source and target languages, source-language text by means of an Dynamic and formal equivalence, equivalent #Source and target languages, target-language text. The ...
of
gene
In biology, the word gene (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a ba ...
s have been reported to occur in spatially segregated locations within the cell, which is otherwise characteristic of eukaryotic but not prokaryotic cells.
Physiology
Sterol synthesis
''G. obscuriglobus'' is one of the few prokaryotes known to synthesize
sterols,
a process critical to the maintenance of eukaryotic cell membranes and ubiquitous in eukaryotes.
The sterols identified in the bacterium,
lanosterol
Lanosterol is a tetracyclic triterpenoid and is the compound from which all animal and fungal steroids are derived. By contrast plant steroids are produced via cycloartenol.
Role in biosynthesis of other steroids
Elaboration of lanosterol under en ...
and
parkeol, are relatively simple compared to eukaryotic sterols; as indicated by
phylogenetic
In biology, phylogenetics (; from Greek φυλή/ φῦλον [] "tribe, clan, race", and wikt:γενετικός, γενετικός [] "origin, source, birth") is the study of the evolutionary history and relationships among or within groups o ...
analysis, the ''G. obscuriglobus'' sterol
biosynthetic pathway
Metabolism (, from el, μεταβολή ''metabolē'', "change") is the set of life-sustaining chemical reactions in organisms. The three main functions of metabolism are: the conversion of the energy in food to energy available to run cell ...
was among the most primitive known at the time it was identified.
Endocytosis
''G. obscuriglobus'' was the first bacterium shown to possess a mechanism for protein import into the cell, analogous to eukaryotic
endocytosis
Endocytosis is a cellular process in which substances are brought into the cell. The material to be internalized is surrounded by an area of cell membrane, which then buds off inside the cell to form a vesicle containing the ingested material. E ...
. Active,
ATP-dependent, likely receptor-mediated import of extracellular proteins has been observed under laboratory conditions, although it is of unknown functional significance. This may suggest that Planctomycetota and eukaryote endocytosis mechanism share a common evolutionary origin, that the two processes may be an example of
convergent evolution
Convergent evolution is the independent evolution of similar features in species of different periods or epochs in time. Convergent evolution creates analogous structures that have similar form or function but were not present in the last com ...
, or that ''G. obscuriglobus'' acquired its endocytotic infrastructure through
horizontal gene transfer
Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between Unicellular organism, unicellular and/or multicellular organisms other than by the ("vertical") transmission of DNA from parent to offsprin ...
; of the three possibilities, the latter is considered unlikely due to statistical features of the bacterial genes associated with the process.
There is disagreement over the possibility that proteins with
homology
Homology may refer to:
Sciences
Biology
*Homology (biology), any characteristic of biological organisms that is derived from a common ancestor
* Sequence homology, biological homology between DNA, RNA, or protein sequences
*Homologous chrom ...
to
clathrin
Clathrin is a protein that plays a major role in the formation of coated vesicles. Clathrin was first isolated and named by Barbara Pearse in 1976. It forms a triskelion shape composed of three clathrin heavy chains and three light chains. Whe ...
s are represented in the ''G. obscuriglobus''
proteome
The proteome is the entire set of proteins that is, or can be, expressed by a genome, cell, tissue, or organism at a certain time. It is the set of expressed proteins in a given type of cell or organism, at a given time, under defined conditions. ...
.
The bacterium's ability to synthesize
sterols may also be involved in its capacity for membrane invaginations and endocytosis because sterols are known to facilitate membrane deformation.
References
External links
Type strain of ''Gemmata obscuriglobus'' at Bac''Dive'' - the Bacterial Diversity Metadatabase
{{Taxonbar, from=Q21349510
Planctomycetota
Bacteria described in 1985