Prokaryotic ubiquitin-like protein (Pup) is a functional analog of
ubiquitin
Ubiquitin is a small (8.6 kDa) regulatory protein found in most tissues of eukaryotic organisms, i.e., it is found ''ubiquitously''. It was discovered in 1975 by Gideon Goldstein and further characterized throughout the late 1970s and 1980s. Fo ...
found in the
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 & Conne ...
''
Mycobacterium tuberculosis''.
Like ubiquitin, Pup serves to direct
protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, res ...
s to the
proteasome for
degradation
Degradation may refer to:
Science
* Degradation (geology), lowering of a fluvial surface by erosion
* Degradation (telecommunications), of an electronic signal
* Biodegradation of organic substances by living organisms
* Environmental degradatio ...
in the Pup-proteasome system (PPS). However, the enzymology of
ubiquitylation
Ubiquitin is a small (8.6 kDa) regulatory protein found in most tissues of eukaryotic organisms, i.e., it is found ''ubiquitously''. It was discovered in 1975 by Gideon Goldstein and further characterized throughout the late 1970s and 1980s. Fou ...
and
pupylation is different, owing to their distinct evolutionary origins. In contrast to the three-step reaction of ubiquitylation, pupylation requires only two steps, and thus only two
enzyme
Enzymes () are proteins that act as biological catalysts by accelerating chemical reactions. The molecules upon which enzymes may act are called substrates, and the enzyme converts the substrates into different molecules known as products ...
s are involved in pupylation. The enzymes involved in
pupylation are descended from
glutamine synthetase
Glutamine synthetase (GS) () is an enzyme that plays an essential role in the metabolism of nitrogen by catalyzing the condensation of glutamate and ammonia to form glutamine:
Glutamate + ATP + NH3 → Glutamine + ADP + phosphate
Glutam ...
.
Similar to ubiquitin, Pup is attached to specific
lysine residues of substrate proteins by
isopeptide bonds; this is called pupylation. It is then recognized by the protein Mycobacterium proteasomal ATPase (Mpa), in a mechanism that induces folding of Pup.
Mpa delivers the substrate protein to the
proteasome for
degradation
Degradation may refer to:
Science
* Degradation (geology), lowering of a fluvial surface by erosion
* Degradation (telecommunications), of an electronic signal
* Biodegradation of organic substances by living organisms
* Environmental degradatio ...
by coupling of ATP hydrolysis.
The discovery of Pup indicates that like
eukaryotes, bacteria may use a small-protein modifier to control protein stability.
The Pup gene encodes a 64–amino acid
protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, res ...
with a molecular size of about 6.9
kDa
The dalton or unified atomic mass unit (symbols: Da or u) is a non-SI unit of mass widely used in physics and chemistry. It is defined as of the mass of an unbound neutral atom of carbon-12 in its nuclear and electronic ground state and at re ...
.
Pup is an
intrinsically disordered protein
In molecular biology, an intrinsically disordered protein (IDP) is a protein that lacks a fixed or ordered three-dimensional structure, typically in the absence of its macromolecular interaction partners, such as other proteins or RNA. IDPs ran ...
. In 2010, scientists at the
Brookhaven National Laboratory
Brookhaven National Laboratory (BNL) is a United States Department of Energy national laboratory located in Upton, Long Island, and was formally established in 1947 at the site of Camp Upton, a former U.S. Army base and Japanese internment c ...
determined the X-ray crystal structure of the complex between Pup and its delivery enzyme Mpa and found that Pup binding to Mpa induces the folding of a unique alpha-helix.
In 2017, the presence of Pup homologs in bacterial species outside of the group of
gram-positive
In bacteriology, gram-positive bacteria are bacteria that give a positive result in the Gram stain test, which is traditionally used to quickly classify bacteria into two broad categories according to their type of cell wall.
Gram-positive bact ...
bacteria was reported.
The Pup homologs were termed
UBact (for Ubiquitin Bacterial), although the distinction has not been proven to be phylogenetically supported by a separate evolutionary origin and is without experimental evidence.
UBact is a homolog of Pup, and is found in several phyla 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 wa ...
bacteria (Pup is found predominantly in the
gram-positive
In bacteriology, gram-positive bacteria are bacteria that give a positive result in the Gram stain test, which is traditionally used to quickly classify bacteria into two broad categories according to their type of cell wall.
Gram-positive bact ...
bacterial phylum
Actinomycetota
The ''Actinomycetota'' (or ''Actinobacteria'') are a phylum of all gram-positive bacteria. They can be terrestrial or aquatic. They are of great economic importance to humans because agriculture and forests depend on their contributions to s ...
).
Ubiquitin bacterial
![UBact family](https://upload.wikimedia.org/wikipedia/commons/6/61/UBact_family.png)
Ubiquitin Bacterial (UBact) is a protein that is homologous to Prokaryotic ubiquitin-like protein (Pup). UBact was recently described by the group of Professor
Aaron Ciechanover
Aaron Ciechanover ( ; he, אהרן צ'חנובר; born October 1, 1947) is an Israeli biologist who won the Nobel Prize in Chemistry for characterizing the method that cells use to degrade and recycle proteins using ubiquitin.
Biography
Earl ...
at the
Technion,
Israel
Israel (; he, יִשְׂרָאֵל, ; ar, إِسْرَائِيل, ), officially the State of Israel ( he, מְדִינַת יִשְׂרָאֵל, label=none, translit=Medīnat Yīsrāʾēl; ), is a country in Western Asia. It is situated ...
.
Ubiquitin
Ubiquitin is a small (8.6 kDa) regulatory protein found in most tissues of eukaryotic organisms, i.e., it is found ''ubiquitously''. It was discovered in 1975 by Gideon Goldstein and further characterized throughout the late 1970s and 1980s. Fo ...
was named for its ubiquitous presence among
eukaryotes, while UBact ('Ubiquitin bacterial') is very limited in occurrence among the vast number of bacterial species.
The terms 'Ubiquitin Bacterial' and 'Prokaryotic ubiquitin-like protein' suggest a molecular similarity between ubiquitin and UBact/Pup which is largely absent.
While ubiquitin assumes a highly stable three-dimensional structure in solution,
Pup has been shown to belong to the group of
intrinsically disordered proteins
In molecular biology, an intrinsically disordered protein (IDP) is a protein that lacks a fixed or ordered three-dimensional structure, typically in the absence of its macromolecular interaction partners, such as other proteins or RNA. IDPs ra ...
.
The establishment of the term UBact is controversial, since to date there is no experimental evidence presented to justify the distinction of UBact from Pup.
The term UBact was denoted because several bacterial species from the phylum Nitrospirae (where UBact was initially identified; e.g., ''
Leptospirillum ferriphilum
''Leptospirillum ferriphilum'' is an iron-oxidising bacterium. It is one of the species responsible for the generation of acid mine drainage
Acid mine drainage, acid and metalliferous drainage (AMD), or acid rock drainage (ARD) is the outflo ...
'') contain both the Pup-proteasome system and a novel ORF-proteasome system that needed to be addressed and therefore was denoted UBact.
The conjugation-proteasome components neighboring the UBact and Pup loci in these Nitrospirae bacteria show weak similarity and are probably not entirely redundant. Figure 2 illustrates the differences between the ''UBact'' and ''Pup'' loci in the representative Nitrospirae bacterium ''Leptospirillum ferrodiazotrophum''. Further analyses of the UBact (and not Pup) locus in ''Leptospirillum ferrodiazotrophum'' revealed its existence and extreme conservation across several gram-negative bacterial phyla, as illustrated in figure 3.
![Alignment of UBact from several bactrerial phyla](https://upload.wikimedia.org/wikipedia/commons/8/80/Alignment_of_UBact_from_several_bactrerial_phyla.png)
In spite of the large difference in sequence, UBact is homologous to Pup and shares several characteristics with it: (i) same genomic location within a cluster of genes homologous to ''Mpa'' -> ''Dop'' -> ''Pup/UBact'' -> ''PrcB'' -> ''PrcA'' -> ''PafA'', (ii) C-terminal sequence that ends exclusively with glutamine or glutamate across bacterial species, (iii) short size (similar to that of ubiquitin) and, (iv) high sequence conservation across tremendous evolutionary distance (a characteristic also in common with ubiquitin). The differences between UBact and Pup are their taxonomic distribution and amino acid sequences. While Pup is predominantly found in the
gram-positive
In bacteriology, gram-positive bacteria are bacteria that give a positive result in the Gram stain test, which is traditionally used to quickly classify bacteria into two broad categories according to their type of cell wall.
Gram-positive bact ...
phylum
Actinomycetota
The ''Actinomycetota'' (or ''Actinobacteria'') are a phylum of all gram-positive bacteria. They can be terrestrial or aquatic. They are of great economic importance to humans because agriculture and forests depend on their contributions to s ...
, UBact was identified only in
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 wa ...
bacteria from the following five phyla:
Nitrospirota
Nitrospirota is a phylum of bacteria. It includes multiple genera, such as '' Nitrospira'', the largest. The first member of this phylum, '' Nitrospira marina'', was discovered in 1985. The second member, '' Nitrospira moscoviensis'', was discove ...
,
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 ...
,
Armatimonadota
''Armatimonadota'' is a phylum of gram-negative bacteria.
History
''Armatimonadota'' was originally described solely on the basis of environmental 16S rRNA gene clone sequences, and was temporarily titled candidate phylum OP10. However, in 20 ...
,
Nitrospinota
Nitrospinota is a bacterial phylum. Despite only few described species, members of this phylum are major nitrite-oxidizing bacteria in surface waters in oceans. By oxidation of nitrite to nitrate they are important in the process of nitrificatio ...
, and
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 ...
. UBact was also identified in the genomes of several
candidatus
In prokaryote nomenclature, ''Candidatus'' (Latin for candidate of Roman office) is used to name prokaryotic phyla that are well characterized but yet-uncultured. Contemporary sequencing approaches, such as 16S sequencing or metagenomics, provide m ...
bacteria, and specifically from the
candidate divisions "
Acetothermia", "
Handelsmanbacteria", "
Fraserbacteria", "
Terrybacteria", "
Poribacteria
Poribacteria are a candidate phylum of bacteria originally discovered in the microbiome of marine sponges (''Porifera''). Poribacteria are Gram-negative primarily aerobic mixotrophs with the ability for oxidative phosphorylation, glycolysis, ...
", "
Parcubacteria", and "
Yanofskybacteria".
With regard to the amino acid sequence, in difference from Pup and
Ubiquitin
Ubiquitin is a small (8.6 kDa) regulatory protein found in most tissues of eukaryotic organisms, i.e., it is found ''ubiquitously''. It was discovered in 1975 by Gideon Goldstein and further characterized throughout the late 1970s and 1980s. Fo ...
, UBact does not contain a di-glycine motif at its C-terminus. Rather, it usually ends with the sequence R
/S /Q(see figure 3).
It took almost ten years since the discovery of Pup in 2008,
to identify UBact. This is probably due to the difference between Pup and UBact amino acids sequences, and because very few bacteria from the five phyla where UBact is found have been sequenced.
Bacteria from the phyla where UBact is found interact with humans,
and are found in the human gut microbiota.
In marine systems, the most frequently encountered nitrogen-oxidizing bacteria are related to the UBact encoding ''Nitrospina gracilis''
From the knowledge accumulated about the Pup-proteasome system and its importance in bacterial durability and disease causing ability,
the homologous UBact-proteasome system is expected to have similar impact on the gram-negative bacteria where it is found. In addition to humans, animals such livestock and fish that eat from the ground or swim in water are expected to be constantly exposed to UBact containing bacteria in the soil and water respectively.
From evolutionary perspective, the finding of the UBact-proteasome system in gram-negative bacteria suggests that either the Pup/UBact-proteasome systems evolved in bacteria prior to the split into gram positive and negative clades over 3000 million years ago
or, that these systems were acquired by different bacterial lineages through
horizontal gene transfer
Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between unicellular and/or multicellular organisms other than by the ("vertical") transmission of DNA from parent to offspring (reproduction). H ...
(s) from a third, yet unknown, organism. In support of the second possibility, two UBact loci were found in the genome of an uncultured anaerobic methanotrophic Archaeon (ANME-1;locu
CBH38808.1and locu
CBH39258.1. More possibilities exist.
Update: UBact is also found in the gram-negative bacterial phylum
Gemmatimonadota
The Gemmatimonadota are a phylum of bacteria established in 2003. The phylum contains two classes Gemmatimonadetes and Longimicrobia.
Species
The type species '' Gemmatimonas aurantiaca'' strain T-27T was isolated from activated sludge in a sewa ...
(e.g.
A0A2E8WA32A0A2E3J6F7A0A2E7JSE3 in the candidate phylum "
Latescibacteria" (previously known as WS3; e.g.
A0A3D2RHP4A0A3D5FTR6A0A3D4H075 an
A0A3B8MMW3, in the phylum "
Abditibacteriota" (previously candidate phylum FBP; e.g.
A0A2S8SU03, and in the phylum Candidatus Bipolaricaulota (e.g.
H5SEU7an
H5SQ95.
See also
*
Ubiquitin
Ubiquitin is a small (8.6 kDa) regulatory protein found in most tissues of eukaryotic organisms, i.e., it is found ''ubiquitously''. It was discovered in 1975 by Gideon Goldstein and further characterized throughout the late 1970s and 1980s. Fo ...
*
SUMO protein
*
Neddylation Neddylation (also NEDDylation) is the process by which the ubiquitin-like protein NEDD8 is conjugated to its target proteins. This process is analogous to ubiquitination, although it relies on its own E1 and E2 enzymes. No NEDD8-specific E3 has yet ...
References
External links
PupDB a database of pupylated proteins and pupylation sites.
{{Posttranslational modification
Bacterial proteins