GNU is an extensive collection of free software (383 packages as of January 2022), which can be used as an operating system or can be used in parts with other operating systems.The use of the completed GNU tools led to the family of operating systems popularly known as Linux. Most of GNU is licensed under the GNU Project's own General Public License (GPL).
GNU is also the project within which the free software concept originated. Richard Stallman, the founder of the project, views GNU as a "technical means to a social end". Relatedly, Lawrence Lessig states in his introduction to the second edition of Stallman's book Free Software, Free Society
that in it Stallman has written about "the social aspects of software
and how Free Software can create community and social justice".
Name
GNU is a recursive acronym for "GNU's Not Unix!", chosen because GNU's design is Unix-like, but differs from Unix by being free software and containing no Unix code. Stallman chose the name by using various plays on words, including the song The Gnu.
History
Development of the GNU operating system was initiated by Richard Stallman while he worked at MIT Artificial Intelligence Laboratory. It was called the GNU Project, and was publicly announced on September 27, 1983, on the net.unix-wizards and net.usoft newsgroups by Stallman.
Software development began on January 5, 1984, when Stallman quit his
job at the Lab so that they could not claim ownership or interfere with
distributing GNU components as free software.
The goal was to bring a completely free software operating system
into existence. Stallman wanted computer users to be free to study the
source code of the software they use, share software with other people,
modify the behavior of software, and publish their modified versions of
the software. This philosophy was published as the GNU Manifesto in March 1985.
Richard Stallman's experience with the Incompatible Timesharing System (ITS), an early operating system written in assembly language that became obsolete due to discontinuation of PDP-10, the computer architecture for which ITS was written, led to a decision that a portable system was necessary. It was thus decided that the development would be started using C and Lisp as system programming languages, and that GNU would be compatible with Unix. At the time, Unix was already a popular proprietary operating system. The design of Unix was modular, so it could be reimplemented piece by piece.
Much of the needed software had to be written from scratch, but
existing compatible third-party free software components were also used
such as the TeX typesetting system, the X Window System, and the Mach microkernel that forms the basis of the GNU Mach core of GNU Hurd (the official kernel of GNU).
With the exception of the aforementioned third-party components, most
of GNU has been written by volunteers; some in their spare time, some
paid by companies, educational institutions, and other non-profit organizations. In October 1985, Stallman set up the Free Software Foundation (FSF). In the late 1980s and 1990s, the FSF hired software developers to write the software needed for GNU.
As GNU gained prominence, interested businesses began
contributing to development or selling GNU software and technical
support. The most prominent and successful of these was Cygnus Solutions, now part of Red Hat.
Many GNU programs have been ported to other operating systems, including proprietary platforms such as Microsoft Windows and macOS. GNU programs have been shown to be more reliable than their proprietary Unix counterparts.
As of January 2022, there are a total of 459 GNU packages
(including decommissioned, 383 excluding) hosted on the official GNU
development site.
In its original meaning,
and one still common in hardware engineering, the operating system is a
basic set of functions to control the hardware and manage things like task scheduling and system calls. In modern terminology used by software developers, the collection of these functions is usually referred to as a kernel,
while an 'operating system' is expected to have a more extensive set of
programmes. The GNU project maintains two kernels itself, allowing the
creation of pure GNU operating systems, but the GNU toolchain is also
used with non-GNU kernels. Due to the two different definitions of the
term 'operating system', there is an ongoing debate concerning the naming of distributions of GNU packages with a non-GNU kernel. (See below.)
The original kernel of GNU Project is the GNU Hurd microkernel, which was the original focus of the Free Software Foundation (FSF).
With the April 30, 2015 release of the Debian GNU/Hurd 2015 distro, GNU now provides all required components to assemble an operating system that users can install and use on a computer.
However, the Hurd kernel is not yet considered production-ready
but rather a base for further development and non-critical application
usage.
Linux-libre
As of 2012, a fork of the Linux kernel became officially part of the GNU Project in the form of Linux-libre, a variant of Linux with all proprietary components removed.
The GNU Project has endorsed Linux-libre distributions, such as gNewSense, Trisquel and Parabola GNU/Linux-libre.
Because of the development status of Hurd, GNU is usually paired with other kernels such as Linux or FreeBSD.
Whether the combination of GNU libraries with external kernels is a GNU
operating system with a kernel (e.g. GNU with Linux), because the GNU
collection renders the kernel into a usable operating system as
understood in modern software development, or whether the kernel is an
operating system unto itself with a GNU layer on top (i.e. Linux with
GNU), because the kernel can operate a machine without GNU, is a matter
of ongoing debate. The FSF maintains that an operating system built
using the Linux kernel and GNU tools and utilities should be considered a variant of GNU, and promotes the term GNU/Linux for such systems (leading to the GNU/Linux naming controversy). This view is not exclusive to the FSF Notably, Debian, one of the biggest and oldest Linux distributions, refers to itself as Debian GNU/Linux.
Copyright, GNU licenses, and stewardship
The GNU Project recommends that contributors assign the copyright for GNU packages to the Free Software Foundation, though the Free Software Foundation considers it acceptable to release small changes to an existing project to the public domain.
However, this is not required; package maintainers may retain copyright
to the GNU packages they maintain, though since only the copyright
holder may enforce the license used (such as the GNU GPL), the copyright
holder in this case enforces it rather than the Free Software
Foundation.
For the development of needed software, Stallman wrote a license called the GNU General Public License (first called Emacs General Public License), with the goal to guarantee users freedom to share and change free software. Stallman wrote this license after his experience with James Gosling and a program called UniPress, over a controversy around software code use in the GNU Emacs program. For most of the 80s, each GNU package had its own license: the Emacs
General Public License, the GCC General Public License, etc. In 1989,
FSF published a single license they could use for all their software,
and which could be used by non-GNU projects: the GNU General Public License (GPL).
This license is now used by most of GNU software, as well as a
large number of free software programs that are not part of the GNU
Project; it also historically has been the most commonly used free software license (though recently challenged by the MIT license).
It gives all recipients of a program the right to run, copy, modify and
distribute it, while forbidding them from imposing further restrictions
on any copies they distribute. This idea is often referred to as copyleft.
In 1991, the GNU Lesser General Public License (LGPL), then known as the Library General Public License, was written for the GNU C Library to allow it to be linked with proprietary software. 1991 also saw the release of version 2 of the GNU GPL. The GNU Free Documentation License (FDL), for documentation, followed in 2000.
The GPL and LGPL were revised to version 3 in 2007, adding clauses to
protect users against hardware restrictions that prevent users from
running modified software on their own devices.
Besides GNU's packages, the GNU Project's licenses can and are used by many unrelated projects, such as the Linux kernel, often used with GNU software. A majority of free software such as the X Window System, is licensed under permissive free software licenses.
Logo
The original GNU logo, drawn by Etienne SuvasaAnniversary logo
The logo for GNU is a gnu head. Originally drawn by Etienne Suvasa, a bolder and simpler version designed by Aurelio Heckert is now preferred.
It appears in GNU software and in printed and electronic documentation
for the GNU Project, and is also used in Free Software Foundation
materials.
There was also a modified version of the official logo. It was created by the Free Software Foundation in September 2013 in order to commemorate the 30th anniversary of the GNU Project.
Although drawing on traditions and philosophies among members of the 1970s hacker culture and academia, Richard Stallman formally founded the movement in 1983 by launching the GNU Project. Stallman later established the Free Software Foundation in 1985 to support the movement.
Philosophy
The
philosophy of the Free Software Movement is based on promoting
collaboration between programmers and computer users. This process
necessitates the rejection of
proprietary software and the promotion of free software.
Stallman notes that this action would not hinder the progression of
technology, as he states, "Wasteful duplication of system programming
effort will be avoided. This effort can go instead into advancing the
state of the art."
Members of the Free Software Movement believe that all software users should have the freedoms listed in The Free Software Definition.
Members hold the belief that it is immoral to prohibit or prevent
people from exercising these freedoms, and that they are required in
creating a community where software users can help each other and have
control over their technology. Regarding proprietary software,
some believe that it is not strictly immoral, citing increased
profitability in the business models available for proprietary software,
along with technical features and convenience.
The Free Software Foundation believes all software needs free documentation, as programmers should have the ability to update manuals to reflect modifications made to the software. Within the movement, the FLOSS Manuals foundation specializes in providing such documentation.
Actions
GNU and Tux mascots around free software supporters at FISL 16
Writing and spreading free software
The
core work of the free software movement is focused on software
development. The free software movement also rejects proprietary
software, refusing to install software that does not give them the
freedoms of free software. According to Stallman, "The only thing in the
software field that is worse than an unauthorised copy of a proprietary
program, is an authorised copy of the proprietary program because this
does the same harm to its whole community of users, and in addition,
usually the developer, the perpetrator of this evil, profits from it."
Building awareness
Some supporters of the free software movement take up public speaking,
or host a stall at software-related conferences to raise awareness of
software freedom. This is seen as important since people who receive
free software, but who are not aware that it is free software, will
later accept a non-free replacement or will add software that is not
free software.
A lot of lobbying work has been done against software patents and expansions of copyright law. Other lobbying focuses directly on the use of free software by government agencies and government-funded projects.
Asia
China
In June 1997, the Society for Study, Application, and Development of Free Software was established under the China Software Industry Association
in Beijing. Through this organization, the website freesoft.cei.gov.cn
was developed, though the website is currently inaccessible on IP
addresses located in the United States. The use of open-source software Linux
in China has moved beyond government and educational institutions and
has extended to other organizations such as financial institutions,
telecommunications, and public security. Several Chinese researchers and
scholars have claimed that the existence of FOSS in China has been
important in challenging the presence of Microsoft, which Guangnan Ni, a member of the Chinese Academy of Engineering stated, "The monopoly of (Microsoft Windows) is even more powerful in China than other places in the world". Yi Zhou, a professor of mathematics at Fudan University,
has also alleged that, "Government procurement of FLOSS for a number of
years in China has compelled Microsoft to cut its prices of Office
software substantially"
India
Government
of India had issued Policy on Adoption of Open Source Software for
Government of India in 2015 to drive uptake within the government. With
the vision to transform India as a Software Product Nation, National
Policy on Software Products-2019 was approved by the Government.
Pakistan
Free
and Open Source Software (Foss) is crucial for countries such as
Pakistan which is set up by Union of Information Technology. For the
case of Pakistan, Pakistan Software Export Board (PSEB) aids in the
creation and advocate of FOSS usage in various government departments in
addition to curbing illegality of copying that is software
piracy.Promotion of adoption of FOSS is essential however it comes with
problems of proprietary anti competition software practices including
indulging in bribing and corruption by government departments.Pakistan
works on the introduction of usage of open type basis of source
Solutions in the curricula in schools and colleges. This is because of
FOSS uniqueness in terms of political, democratic and social varieties
of aspect regarding information communication and technology.
North America
United States
In
the United States, there have been efforts to pass legislation at the
state level encouraging the use of free software by state government
agencies.
On January 11, 2022, two bills were shown on the New Hampshire
legislating floor. The first bill called “HB 1273” was introduced by
Democratic New Hampshire representative Eric Gallager, the bill
prioritized “replacing proprietary software used by state agencies with
free software.” Gallager stated that to an extent, the proposed
legislation will help distinguish “free software" and “open-source
software”, this will also put these two into state regulation. The
second bill called “HB 1581” was proposed by Grafton Republican
representative Lex Berezhny. The bill would’ve restored a requisite
forcing “state agencies to use proprietary software” and as Lex put it,
“when it is the most effective solution.” He also said that requisite
was happening between 2012 and 2018. According to the Concord Monitor,
the state of New Hampshire had an already “thriving open source
software community” with a view of “live free or die” but they had
difficulty getting that notion with the state.
South America
Peru
Congressmen Edgar David Villanueva and Jacques Rodrich Ackerman have been instrumental in introducing free software in Peru, with bill 1609 on "Free Software in Public Administration". The incident invited the attention of Microsoft,
Peru, whose general manager wrote a letter to Villanueva. His response
received worldwide attention and is seen as a classic piece of
argumentation favouring use of free software in governments.
Uruguay
Uruguay
has a sanctioned law requiring that the state give priority to free
software. It also requires that information be exchanged in open formats.
Venezuela
The Government of Venezuela
implemented a free software law in January 2006. Decree No. 3,390
mandated all government agencies to migrate to free software over a
two-year period.
Europe
Publiccode.eu
is a campaign launched demanding a legislation requiring that publicly
financed software developed for the public sector be made publicly
available under a Free and Open Source Software licence. If it is public
money, it should be public code as well.
Free Software events happening all around the world connects people
to increase visibility for Free software projects and foster
collaborations.
Economics
The free software movement has been extensively analyzed using economic methodologies, including perspectives from heterodox economics. Of particular interest to economists is the willingness of programmers in the free software movement to work, often producing higher-quality than proprietary programmers, without financial compensation.
Gabriella Coleman has emphasized the importance of accreditation, respect, and honour
within the free software community as a form of compensation for
contributions to projects, over and against financial motivations.
The Swedish Marxian economist Johan Söderberg has argued that the free software movement represents a complete alternative to capitalism
that may be expanded to create a post-work society. He argues that the
combination of a manipulation of intellectual property law and private property to make goods available to the public and a thorough blend between labor and fun make the free software movement a communist economy.
Subgroups and schisms
Since its inception, there is an ongoing contension between the many FLOSS organizations (FSF, OSI, Debian, Mozilla Foundation, Apache Foundation,
etc.) within the free software movement, with the main conflicts
centered around the organization's needs for compromise and pragmatism
rather than adhering to founding values and philosophies.
The Open Source Initiative (OSI) was founded in February 1998 by Eric Raymond and Bruce Perens to promote the term "open-source software" as an alternative term for free software.
The OSI aimed to address the perceived shortcomings and ambiguity of
the term "free software", as well as shifting the focus of free software
from a social and ethical issue to instead emphasize open source as a
superior model for software development. The latter became the view of Eric Raymond and Linus Torvalds,
while Bruce Perens argued that open source was meant to popularize free
software under a new brand and called for a return to basic ethical
principles.
Some free software advocates use the terms "Free and Open-Source Software"
(FOSS) or "Free/Libre and Open-Source Software" (FLOSS) as a form of
inclusive compromise, which brings free and open-source software
advocates together to work on projects cohesively. Some users believe
this is an ideal solution in order to promote both the user's freedom
with the software and the pragmatic efficiency of an open-source
development model. This view is reinforced by fact that majority of OSI-approved licenses and self-avowed open-source programs are also compatible with the free software formalisms and vice versa.
While free and open source software are often linked together,
they offer two separate ideas and values. Richard Stallman has referred
to open source as "a non-movement", as it "does not campaign for anything".
"Open source" addresses software being open as a practical
question rather than an ethical dilemma – non-free software is not the
best solution but nonetheless a solution. The free software movement
views free software as a moral imperative: that proprietary software
should be rejected, and that only free software should be developed and
taught in order to make computing technology beneficial to the general
public.
Although the movements have differing values and goals,
collaborations between the Free Software Movement and Open Source
Initiative have taken place when it comes to practical projects.
By 2005, Richard Glass considered the differences to be a "serious
fracture" but "vitally important to those on both sides of the fracture"
and "of little importance to anyone else studying the movement from a
software engineering perspective" since they have had "little effect on
the field".
Criticism and controversy
Principle compromises
Eric Raymond
criticises the speed at which the free software movement is
progressing, suggesting that temporary compromises should be made for
long-term gains. Raymond argues that this could raise awareness of the
software and thus increase the free software movement's influence on
relevant standards and legislation.
Richard Stallman, on the other hand, sees the current level of compromise as a greater cause for worry.
Stallman said that this is where people get the misconception of
"free": there is no wrong in programmers' requesting payment for a
proposed project, or charging for copies of free software.
Restricting and controlling the user's decisions on use is the actual
violation of freedom. Stallman defends that in some cases, monetary
incentive is not necessary for motivation since the pleasure in
expressing creativity is a reward in itself. Conversely, Stallman admits that it is not easy to raise money for free software projects.
"Viral" copyleft licensing
The free software movement champions copyleft licensing schema (often pejoratively called "viral licenses"). In its strongest form, copyleft mandates that any works derived
from copyleft-licensed software must also carry a copyleft license, so
the license spreads from work to work like a computer virus might spread
from machine to machine. Stallman has previously stated his opposition
to describing the GNU GPL as "viral". These licensing terms can only be enforced through asserting copyrights.
Critics of copyleft licensing challenge the idea that restricting
modifications is in line with the free software movement's emphasis on
various "freedoms", especially when alternatives like MIT, BSD, and Apache licenses are more permissive. Proponents enjoy the assurance that copylefted work cannot usually be incorporated into non-free software projects.
They emphasize that copyleft licenses may not attach for all uses and
that in any case, developers can simply choose not to use
copyleft-licensed software.
FLOSS license proliferation is a serious concern in the FLOSS domain due to increased complexity of license compatibility considerations which limits and complicates source code reuse between FLOSS projects. The OSI and the FSF maintain their own lists of dozens of existing and acceptable FLOSS licenses.
There is an agreement among most that the creation of new licenses
should be minimized and those created should be made compatible with the
major existing FLOSS licenses. Therefore, there was a strong
controversy around the update of the GNU GPLv2 to the GNU GPLv3 in 2007, as the updated license is not compatible with the previous version. Several projects (mostly of the open source faction like the Linux kernel) decided to not adopt the GPLv3 while almost all of the GNU project's packages adopted it.
In eukaryotes, there are six members of the tubulin superfamily, although not all are present in all species. Both α and β tubulins have a mass of around 50 kDa and are thus in a similar range compared to actin (with a mass of ~42 kDa). In contrast, tubulin polymers (microtubules) tend to be much bigger than actin filaments due to their cylindrical nature.
Tubulin was long thought to be specific to eukaryotes. More recently, however, several prokaryotic proteins have been shown to be related to tubulin.
Characterization
Tubulin is characterized by the evolutionarily conserved Tubulin/FtsZ family, GTPaseprotein domain.
This GTPase protein domain is found in all eukaryotic tubulin chains, as well as the bacterial protein TubZ, the archaeal protein CetZ, and the FtsZ protein family widespread in bacteria and archaea.
α- and β-tubulin polymerize into dynamic microtubules. In eukaryotes, microtubules are one of the major components of the cytoskeleton, and function in many processes, including structural support, intracellular transport, and DNA segregation.
Comparison
of the architectures of a 5-protofilament bacterial microtubule (left;
BtubA in dark blue; BtubB in light-blue) and a 13-protofilament
eukaryotic microtubule (right; α-tubulin in white; β-tubulin in black).
Seams and start-helices are indicated in green and red, respectively.
Microtubules are assembled from dimers of α- and β-tubulin. These subunits are slightly acidic, with an isoelectric point between 5.2 and 5.8. Each has a molecular weight of approximately 50 kDa.
To form microtubules, the dimers of α- and β-tubulin bind to GTP and assemble onto the (+) ends of microtubules while in the GTP-bound state.
The β-tubulin subunit is exposed on the plus end of the microtubule,
while the α-tubulin subunit is exposed on the minus end. After the
dimer is incorporated into the microtubule, the molecule of GTP bound to
the β-tubulin subunit eventually hydrolyzes into GDP through inter-dimer contacts along the microtubule protofilament.
The GTP molecule bound to the α-tubulin subunit is not hydrolyzed
during the whole process. Whether the β-tubulin member of the tubulin
dimer is bound to GTP or GDP influences the stability of the dimer in
the microtubule. Dimers bound to GTP tend to assemble into microtubules,
while dimers bound to GDP tend to fall apart; thus, this GTP cycle is
essential for the dynamic instability of the microtubule.
Bacterial microtubules
Homologs of α- and β-tubulin have been identified in the Prosthecobactergenus of bacteria. They are designated BtubA and BtubB to identify them as bacterial tubulins. Both exhibit homology to both α- and β-tubulin. While structurally highly similar to eukaryotic tubulins, they have several unique features, including chaperone-free folding and weak dimerization. Cryogenic electron microscopy showed that BtubA/B forms microtubules in vivo,
and suggested that these microtubules comprise only five
protofilaments, in contrast to eukaryotic microtubules, which usually
contain 13. Subsequent in vitro studies have shown that BtubA/B forms four-stranded 'mini-microtubules'.
DNA segregation
Cell division
Prokaryotic division
FtsZ is found in nearly all Bacteria and Archaea, where it functions in cell division,
localizing to a ring in the middle of the dividing cell and recruiting
other components of the divisome, the group of proteins that together
constrict the cell envelope to pinch off the cell, yielding two daughter
cells. FtsZ can polymerize into tubes, sheets, and rings in vitro, and forms dynamic filaments in vivo.
TubZ functions in segregating low copy-number plasmids
during bacterial cell division. The protein forms a structure unusual
for a tubulin homolog; two helical filaments wrap around one another. This may reflect an optimal structure for this role since the unrelated plasmid-partitioning protein ParM exhibits a similar structure.
Cell shape
CetZ functions in cell shape changes in pleomorphicHaloarchaea. In Haloferax volcanii,
CetZ forms dynamic cytoskeletal structures required for differentiation
from a plate-shaped cell form into a rod-shaped form that exhibits
swimming motility.
Types
Eukaryotic
The tubulin superfamily contains six families (alpha-(α), beta-(β), gamma-(γ), delta-(δ), epsilon-(ε), and zeta-(ζ) tubulins).
All drugs that are known to bind to human tubulin bind to β-tubulin. These include paclitaxel, colchicine, and the vinca alkaloids, each of which have a distinct binding site on β-tubulin.
In addition, several anti-worm drugs preferentially target the
colchicine site of β-Tubulin in worm rather than in higher eukaryotes.
While mebendazole still retains some binding affinity to human and Drosophila β-tubulin, albendazole almost exclusively binds to the β-tubulin of worms and other lower eukaryotes.
Class III β-tubulin is a microtubule element expressed exclusively in neurons, and is a popular identifier specific for neurons in nervous tissue. It binds colchicine much more slowly than other isotypes of β-tubulin.
β1-tubulin, sometimes called class VI β-tubulin, is the most divergent at the amino acid sequence level.
It is expressed exclusively in megakaryocytes and platelets in humans
and appears to play an important role in the formation of platelets.
When class VI β-tubulin were expressed in mammalian cells, they cause
disruption of microtubule network, microtubule fragment formation, and
can ultimately cause marginal-band like structures present in
megakaryocytes and platelets.
Katanin
is a protein complex that severs microtubules at β-tubulin subunits,
and is necessary for rapid microtubule transport in neurons and in
higher plants.
γ-Tubulin, another member of the tubulin family, is important in the nucleation and polar orientation of microtubules. It is found primarily in centrosomes and spindle pole bodies,
since these are the areas of most abundant microtubule nucleation. In
these organelles, several γ-tubulin and other protein molecules are
found in complexes known as γ-tubulin ring complexes
(γ-TuRCs), which chemically mimic the (+) end of a microtubule and thus
allow microtubules to bind. γ-tubulin also has been isolated as a dimer
and as a part of a γ-tubulin small complex (γTuSC), intermediate in
size between the dimer and the γTuRC. γ-tubulin is the best understood
mechanism of microtubule nucleation, but certain studies have indicated
that certain cells may be able to adapt to its absence, as indicated by mutation and RNAi
studies that have inhibited its correct expression. Besides forming a
γ-TuRC to nucleate and organize microtubules, γ-tubulin can polymerize
into filaments that assemble into bundles and meshworks.
Delta (δ) and epsilon (ε) tubulin have been found to localize at centrioles and may play a role in centriole structure and function, though neither is as well-studied as the α- and β- forms.
Zeta-tubulin (IPR004058)
is present in many eukaryotes, but missing from others, including
placental mammals. It has been shown to be associated with the basal
foot structure of centrioles in multiciliated epithelial cells.
Prokaryotic
BtubA/B
BtubA (Q8GCC5) and BtubB (Q8GCC1) are found in some bacterial species in the Verrucomicrobiota genus Prosthecobacter.
Their evolutionary relationship to eukaryotic tubulins is unclear,
although they may have descended from a eukaryotic lineage by lateral gene transfer.
Compared to other bacterial homologs, they are much more similar to
eukaryotic tubulins. In an assembled structure, BtubB acts like
α-tubulin and BtubA acts like β-tubulin.
TubZ (Q8KNP3; pBt156) was identified in Bacillus thuringiensis as essential for plasmid maintenance. It binds to a DNA-binding protein called TubR (Q8KNP2; pBt157) to pull the plasmid around.
Phages of the genus Phikzlikevirus, as well as a Serratia phage PCH45, use a shell protein (Q8SDA8) to build a nucleus-like
structure called the phage nucleus. This structure encloses DNA as well
as replication and transcription machinery. It protects phage DNA from
host defenses like restriction enzymes and type I CRISPR-Cas systems. A spindle-forming tubulin, variously named PhuZ (B3FK34) and gp187, centers the nucleus in the cell.
Odinarchaeota tubulin
Asgard archaea
tubulin from hydrothermal-living Odinarchaeota (OdinTubulin) was
identified as a genuine tubulin. OdinTubulin forms protomers and
protofilaments most similar to eukaryotic microtubules, yet assembles
into ring systems more similar to FtsZ, indicating that OdinTubulin may represent an evolution intermediate between FtsZ and microtubule-forming tubulins.
Tubulins are targets for anticancer drugs such as vinblastine and vincristine, and paclitaxel. The anti-worm drugsmebendazole and albendazole as well as the anti-gout agent colchicine bind to tubulin and inhibit microtubule formation. While the former ultimately lead to cell death in worms, the latter arrests neutrophil motility and decreases inflammation in humans. The anti-fungal drug griseofulvin targets microtubule formation and has applications in cancer treatment.
Nowadays there are many scientific investigations of the acetylation done in some microtubules, specially the one by α-tubulin N-acetyltransferase (ATAT1)
which is being demonstrated to play an important role in many
biological and molecular functions and, therefore, it is also associated
with many human diseases, specially neurological diseases.
Natural enemies—predators, pathogens, and parasitoids
that attack plant-feeding insects—can benefit plants by hindering the
feeding behavior of the harmful insect. It is thought that many plant
traits have evolved in response to this mutualism
to make themselves more attractive to natural enemies. This recruitment
of natural enemies functions to protect against excessive herbivory and
is considered an indirect plant defense mechanism. Traits attractive to natural enemies can be physical, as in the cases of domatia and nectaries; or chemical, as in the case of induced plant volatile chemicals that help natural enemies pinpoint a food source.
Humans can take advantage of tritrophic interactions in the biological control of insect pests.
Chemical mechanisms of enemy attraction
Plants produce secondary metabolites known as allelochemicals. Rather than participating in basic metabolic processes, they mediate interactions between a plant and its environment, often attracting, repelling, or poisoning insects. They also help produce secondary cell wall components such as those that require amino acid modification.
In a tritrophic system, volatiles,
which are released into the air, are superior to surface chemicals in
drawing foraging natural enemies from afar. Plants also produce root
volatiles which will drive tritrophic interactions between below-ground
herbivores and their natural enemies. Some plant volatiles can be smelled by humans and give plants like basil, eucalyptus, and pine their distinctive odors. The mixture and ratios of individual volatiles emitted by a plant under given circumstances (also referred to as synomones
in the context of natural enemy attraction) is referred to as a
volatile profile. These are highly specific to certain plant species and
are detectable meters from the source. Predators and parasitoids
exploit the specificity of volatile profiles to navigate the complex
infochemical signals presented by plants in their efforts to locate a
particular prey species.
The production of volatiles is likely to be beneficial given two
conditions: that they are effective in attracting natural enemies and
that the natural enemies are effective in removing or impeding
herbivores. However, volatile chemicals may not have evolved initially
for this purpose; they act in within-plant signaling, attraction of pollinators, or repulsion of herbivores that dislike such odors.
Induced defenses
Jasmonic acid, a herbivore-induced plant volative, helps to attract natural enemies of plant pests.
When an herbivore starts eating a plant, the plant may respond by increasing its production of volatiles or changing its volatile profile. This plasticity is controlled by either the jasmonic acid pathway or the salicylic acid pathway, depending largely on the herbivore; these substances are often called herbivore-induced plant volatiles (HIPVs). The plant hormone jasmonic acid
increases in concentration when plants are damaged and is responsible
for inducing the transcription of enzymes that synthesize secondary
metabolites. This hormone also aids in the production of defensive proteins such as α-amylase inhibitors, as well as lectins. Since α-amylase breaks down starch, α-amylase inhibitors prevent insects from deriving nutrition from starch. Lectins likewise interfere with insect nutrient absorption as they bind to carbohydrates.
Though volatiles of any kind have an attractive effect on natural
enemies, this effect is stronger for damaged plants than for undamaged
plants,
perhaps because induced volatiles signal definitive and recent
herbivore activity. The inducibility gives rise to the idea that plants
are sending out a "distress call" to the third trophic level in times of
herbivore attack.
Natural enemies can distinguish between mechanical tissue damage,
which might occur during events other than herbivory, and damage that
is the direct result of insect feeding behavior. The presence of
herbivore saliva or regurgitant
mediates this differentiation, and the resulting chemical pathway leads
to a stronger natural enemy response than mechanical damage could.
The reliability of HIPVs in broadcasting the location of prey means
that, for many foraging enemies, induced plant volatiles are more
attractive than even the odors emitted by the prey insect itself.
Plants are able to determine what types of herbivore species are
present, and will react differently given the herbivore's traits. If
certain defense mechanisms are not effective, plants may turn to
attracting natural enemies of herbivore populations. For example, wild
tobacco plants use nicotine, a neurotoxin, to defend against herbivores. However, when faced with nicotine-tolerant herbivores, they will attract natural enemies.
Local and systemic signals
When
herbivores trigger an inducible chemical defense pathway, the resulting
HIPVs may be emitted either from the site of feeding damage (local
induction) or from undamaged tissues belonging to a damaged plant
(systemic induction). For example, when an herbivore feeds on a single
corn seedling leaf, the plant will emit volatiles from all its leaves,
whether or not they too have been damaged. Locally induced defenses aid
parasitoids in targeting their foraging behaviors to the exact location
of the herbivore on the plant. Systemic defenses are less spatially
specific and may serve to confuse the enemy once the source plant is
located. A plant might employ both local and systemic responses
simultaneously.
Morphological mechanisms of enemy attraction
Domatia
A hairless foveole domatium in the leaf underside of Guioa acutifolia
Natural enemies must survive long enough and respond quickly enough
to plant volatiles in order to benefit the plant through predatory
behavior. Certain plant structures, called domatia,
can selectively reinforce mutualisms with natural enemies and increase
the fitness benefit they receive from that mutualism by ensuring the
survival and proximity of natural enemies. Domatia provide a kind of
housing or refuge for predators from both abiotic stressors,
such as desiccation, and biotic stressors, such as predation from
higher-order predators. Therefore, they not only ensure better survival,
but eliminate the time required for natural enemies to locate and
travel to the damaged plant. Natural enemies that make use of domatia
are often said to serve as "bodyguards" for the plant on or in which
they live. Domatia may be as well-developed as acacia tree thorns or as
simple and incidental as a depression or crevice in a leaf stem, but
they are distinguishable from galls and other similar structures in that they are not induced by the insect but formed constitutively by the plant.
Nutritional rewards
As long as natural enemies have some potential to be omnivorous,
plants can provide food resources to encourage their retention and
increase the impact they have on herbivore populations. This potential,
however, can hinge on a number of the insect's traits. For example, hemipteran predators can use their sucking mouthparts to make use of leaves, stems, and fruits, but spiders with chelicerae cannot. Still, insects widely considered to be purely carnivorous have been observed to diverge from expected feeding behavior.
Some plants simply tolerate a low level of herbivory by natural enemies
for the service they provide in ridding the plant of more serious
herbivores. Others, however, have structures thought to serve no purpose
other than attracting and provisioning natural enemies. These
structures derive from a long history of coevolution between the first and third trophic levels. A good example is the extrafloral nectaries that many myrmecophytes and other angiosperms
sport on leaves, bracts, stems, and fruits. Nutritionally, extrafloral
nectaries are similar to floral nectaries, but they do not lead the
visiting insect to come into contact with pollen. Their existence is
therefore not the product of a pollinator–plant mutualism, but rather a
tritrophic, defensive interaction.
Herbivore sequestration of plant defensive compounds
Multitrophic interaction: Euphydryas editha taylori larvae sequester defensive compounds from specific types of plants they consume to protect themselves from bird predators
The field of chemical ecology has elucidated additional types of plant multitrophic interactions that entail the transfer of defensive compounds across multiple trophic levels. For example, certain plant species in the Castilleja and Plantago genera have been found to produce defensive compounds called iridoid glycosides that are sequestered in the tissues of the Taylor's checkerspot butterflylarvae that have developed a tolerance for these compounds and are able to consume the foliage of these plants. These sequestered iridoid glycosides then confer chemical protection against bird predators to the butterfly larvae. Another example of this sort of multitrophic interaction in plants is the transfer of defensive alkaloids produced by endophytes living within a grass host to a hemiparasitic plant that is also using the grass as a host.
Exploitation of tritrophic interactions can benefit agricultural systems. Biocontrol of crop pests can be exerted by the third trophic level, given an adequate population of natural enemies. However, the widespread use of pesticides or Bt crops can undermine natural enemies’ success. In some cases, populations of predators and parasitoids are decimated,
necessitating even greater use of insecticide because the ecological service they provided in controlling herbivores has been lost.
Even when pesticides are not widely used, monocultures often have difficulty support natural enemies in great enough numbers for them to diminish pest populations. A lack of diversity
in the first trophic level is linked to low abundance in the third
because alternative resources that are necessary for stable, large
natural enemy populations are missing from the system. Natural enemy
diets can be subsidized by increasing landscape diversity through companion planting, border crops, cover crops, intercropping, or tolerance of some weed growth. When nectar or other sugar-rich resources are provided, the natural enemy population thrives.
Biological control
Morphological plant characteristics and natural enemy success
Beyond domatia and nutritional rewards, other plant characteristics
influence the colonization of plants by natural enemies. These can
include the physical size, shape, density, maturity, colour, and texture
of a given plant species. Specific plant features such as the hairiness
or glossiness of vegetation can have mixed effects on different natural
enemies. For example, trichomes
decrease hunting efficiency of many natural enemies, as trichomes tend
to slow or prevent movement due to the physical obstacles they present
or the adhesive secretions they produce. However, sometimes the prey
species may be more impeded than the predator. For example, when the whitefly prey of the parasitoid Encarsia formosa is slowed by plant hairs, the parasitoid can detect and parasitize a higher number of juvenile whiteflies.
Many predatory coccinelid
beetles have a preference for the type of leaf surface they frequent.
Presented with the opportunity to land on glossy or hairy Brassica oleracea
foliage, the beetles prefer the glossy foliage as they are better able
to cling to these leaves. Studies are evaluating the effect of various
plant genotypes on natural enemies.
Volatile organic compounds
Two
ways the release of volatile organic compounds (VOCs) may benefit
plants are the deterrence of herbivores and the attraction of natural
enemies.
Synthetic products could replicate the distinct VOC profiles released
by different plants; these products could be applied to plants suffering
from pests that are targeted by the attracted natural enemy.
This could cause natural enemies to enter crops that are occupied by
pest populations that would otherwise likely remain undetected by the
natural enemies.
The four elements that must be considered before manipulating
VOCs are as follows: The VOCs must effectively aid the natural enemy in
finding the prey; the pest must have natural enemies present; the
fitness cost of potentially attracting more herbivores must be exceeded
by attracting natural enemies; and the natural enemies must not be
negatively affected by direct plant defenses that may be present.
Extrafloral nectaries
A pair of extrafloral nectaries secreting nectar from a Passiflora edulis leaf
The level of domestication of cotton plants correlates to indirect
defense investment in the form of extrafloral nectaries. Wild varieties
produce higher volumes of nectar and attract a wider variety of natural
enemies.
Thus, the process of breeding new cotton varieties has overlooked
natural resistance traits in the pursuit of high-yielding varieties that
can be protected by pesticides. Plants bearing extrafloral nectaries
have lower pest levels along with greater levels of natural enemies. Feeding by herbivores can directly induce nectar production.
These findings illustrate the potential benefits that could be gained
through incorporating the desirable genetics of wild varieties into
cultivated varieties.
Domatia
Certain
tropical plants host colonies of ants in their hollow domatia and
provide the ants with nutrition delivered from nectaries or food bodies.
These ant colonies have become dependent on the host plants for their
survival and therefore actively protect the plant; this protection can
take the form of killing or warding off pests, weeds, and certain fungal
pathogens. Chinese citrus farmers have capitalized on this mutualistic
relationship for many years by incorporating artificial ant nests into
their crops to suppress pests.
Parasitoids
A Brazilian parasitoid wasp raising its ovipositor.
Parasitoids have successfully been incorporated into biological pest control
programs for many years. Plants can influence the effect of parasitoids
on herbivores by releasing chemical cues that attract parasitoids and
by providing food sources or domatia.
Certain parasitoids may be dependent on this plant relationship.
Therefore, in agricultural areas where parasitoid presence is desired,
ensuring the crops being grown meet all of these requirements is likely
to promote higher parasitoid populations and better pest control.
Parasitized aphids with visible parasitoid wasp exit holes.
In a sugar beet
crop, when only beets were grown, few aphids were parasitized. However,
when collard crops were grown next to the sugar beets, parasitism of
aphids increased. Collard crops release more VOCs than sugar beets. As a
result, the companion collard plants attract more aphid parasitoids,
which kill aphids in both the collard and the nearby sugar beets.
In a related study, ethylene and other compounds released by rice plants in response to brown planthopper feeding attracted a facultative parasitoid that parasitizes brown planthopper eggs.
In another study, the presence of plant extrafloral nectaries
in cotton crops caused parasitoids to spend more time in the cotton and
led to the parasitization of more moth larva than in cotton crops with
no nectaries. Since the publication of this study, most farmers have
switched to cotton varieties with nectaries.
A separate study found that a naturalized cotton variety emitted seven
times more VOCs than cultivated cotton varieties when experiencing
feeding damage. It is unknown whether this generalizes to other crops; there are cases of other crops that do not show the same trend.
These findings reveal the specific variables a farmer can
manipulate to influence parasitoid populations and illustrate the
potential impact parasitoid habitat management can have on pest control.
In the case of cotton and other similar high-VOC crop scenarios, there
is interest in genetically engineering the chemical pathways of
cultivated varieties to selectively produce the high VOC's that were
observed in the naturalized varieties in order to attract greater
natural enemy populations. This presents challenges but could produce
promising pest control opportunities.
Insect pathogens
A fly infected by a Cordyceps entomopathogenic fungi with fruiting body structures present
Entomopathogens are another group of organisms that are influenced by
plants. The extent of the influence largely depends on the evolutionary
history shared between the two and the pathogens' method of infection
and survival duration outside of a host. Different insect host plants
contain compounds that cause modulate insect mortality when certain
entomopathogens are simultaneously injected. Increases in mortality of
up to 50-fold have been recorded. However, certain plants influence
entomopathogens in negative ways, reducing their efficacy.
It is primarily the leaf surface of the plant that influences the entomopathogen; plants can release various exudates, phytochemicals, and alleolochemicals through their leaves, some of which have the ability to inactivate certain entomopathogens.
In contrast, in other plant species, leaf characteristics can increase
the efficacy of entomopathogens. For example, the mortality of pea
aphids was higher in the group of aphids that were found on plants with
fewer wax exudates than in those on plants with more wax exudates. This
reduced waxiness increases the transmission of Pandora neoaphidusconidia from the plant to the aphids.
Feeding-induced volatiles emitted by different plants increase the amount of spores released by certain entomopathogenic fungi,
increasing the likelihood of infection of some herbivores but not
others. Plants can also influence pathogen efficacy indirectly, and this
typically occurs either by increasing the susceptibility of the
herbivore hosts or by changing their behavior. This influence can often
take the form of altered growth rates, herbivore physiology, or feeding
habits. Thus, there are various ways that host plant species can
influence entomopathogenic interactions.
In one study, brassicas were found to defend themselves by acting as a vector
for entomopathogens. Virus-infected aphids feeding on the plants
introduce a virus into the phloem. The virus is passively transported in
the phloem and carried throughout the plant. This causes aphids feeding
apart from the infected aphids to become infected as well. This finding
offers the possibility of injecting crops with compatible
entomopathogenic viruses to defend against susceptible insect pests.
Below-ground tritrophic interactions
Less
studied than above-ground interactions, but proving to be increasingly
important, are the below-ground interactions that influence plant
defense. There is a complex network of signal transduction pathways
involved in plant responses to stimuli, and soil microbes can influence
these responses. Certain soil microbes aid plant growth, producing
increased tolerance to various environmental stressors, and can protect
their host plants from many different pathogens by inducing systemic
resistance.
Organisms in above- and below-ground environments can interact
indirectly through plants. Many studies have shown both the positive and
negative effects that one organism in one environment can have on other
organisms in the same or opposite environment, with the plant acting as
the intermediary.
A mycorhizal association with a plant root
The colonization of plant roots with mycorhizae
typically results in a mutualistic relationship between the plant and
the fungus, inducing a number of changes in the plant. Such colonization
has a mixed impact on herbivores; insects with different feeding
methods are affected differently, some positively and others negatively. The mycorhizal species involved also matters. One common species, Rhizophagus irregularis,
has been observed to have a negative effect on the feeding success of
chewing herbivores, whereas other species studied have positive effects.
The roots of some maize plants produce a defense chemical when
roots are damaged by leaf beetle larvae; this chemical attracts the entomopathogenic nematode species Heterorhabditis megidis.
Only certain maize varieties produce this chemical; plants that release
the chemical see up to five times as much parasitization of leaf beetle
larvae as those that do not. Incorporating these varieties or their
genes into commercial maize production could increase the efficacy of
nematode treatments.
Further studies suggest that the plant-emitted chemicals act as
the primary source of attractant to the nematodes. Herbivores are
believed to have evolved to evade detection on the part of the
nematodes, whereas the plants have evolved to release highly attractive
chemical signals. A high degree of specificity is involved; species that
make up these tritrophic interactions have evolved with one another
over a long period of time and as a result have close
interrelationships.
Microorganisms can also influence tritrophic interactions. The bacterium Klebsiella aerogenes produces the volatile 2,3-butanediol, which modulates interactions between plants, pathogens, and insects.
When maize plants are grown in a soil culture containing the bacterium
or the plants are inoculated with the bacterium, the maize is more
resistant to the fungus Setosphaeria turcica. The bacterium does not deter insect herbivory; it actually increases weight gain and leaf consumption in the caterpillar Spodoptera littoralis. However, the parasitic wasp Cotesia marginiventris
is attracted more readily to maize plants grown in soil cultures
containing either the volatile-producing bacterium or pure
2,3-butanediol.
Considerations in utilizing tritrophic interactions in biological control
Sustainable
crop production is becoming increasingly important, if humans are to
support a growing population and avoid a collapse of production systems.
While the understanding and incorporation of tritrophic interactions in
pest control offers a promising control option, the sustainable
biological control of pests requires a dynamic approach that involves
diversity in all of the species present, richness in natural enemies,
and limited adverse activity (i.e., minimal pesticide use). This
approach is especially important in conservation biological control
efforts.
There are typically more than three trophic levels at play in a
given production setting, so the tritrophic interaction model may
represent an oversimplification.
Furthermore, ecological complexity and interactions between species of
the same trophic level can come into play. Research thus far has had a
relatively narrow focus, which may be suitable for controlled
environments such as greenhouses but which has not yet addressed
multi-generational plant interactions with dynamic communities of
organisms.
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