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- 5.1: Unicellular Eukaryotic Microorganisms
- Protists are a diverse, polyphyletic group of eukaryotic organisms. Protists may be unicellular or multicellular. They vary in how they get their nutrition, morphology, method of locomotion, and mode of reproduction. Important structures of protists include contractile vacuoles, cilia, flagella, pellicles, and pseudopodia; some lack organelles such as mitochondria. Taxonomy of protists is changing rapidly as relationships are reassessed using newer techniques.
- 5.2: Parasitic Helminths
- Helminth parasites are included within the study of microbiology because they are often identified by looking for microscopic eggs and larvae. The two major groups of helminth parasites are the roundworms (Nematoda) and the flatworms (Platyhelminthes). Nematodes are common intestinal parasites often transmitted through undercooked foods, although they are also found in other environments. Platyhelminths include tapeworms and flukes, which are often transmitted through undercooked meat.
- 5.3: Fungi
- The fungi include diverse saprotrophic eukaryotic organisms with chitin cell walls. Fungi can be unicellular or multicellular; some (like yeast) and fungal spores are microscopic, whereas some are large and conspicuous. Reproductive types are important in distinguishing fungal groups. Medically important species exist in the four fungal groups Zygomycota, Ascomycota, Basidiomycota, and Microsporidia.
- 5.4: Algae
- Algae are a diverse group of photosynthetic eukaryotic protists Algae may be unicellular or multicellular Large, multicellular algae are called seaweeds but are not plants and lack plant-like tissues and organs Although algae have little pathogenicity, they may be associated with toxic algal blooms that can and aquatic wildlife and contaminate seafood with toxins that cause paralysis.
- 5.5: Lichens
- Lichens are a symbiotic association between a fungus and an algae or a cyanobacterium. The symbiotic association found in lichens is currently considered to be a controlled parasitism, in which the fungus benefits and the algae or cyanobacterium is harmed. Lichens are slow growing and can live for centuries in a variety of habitats. Lichens are environmentally important, helping to create soil, providing food, and acting as indicators of air pollution.
Thumbnail: Mold growing on a clementine. Image used with permission (CC SA-BY 3.0; NotFromUtrecht).
Chapter 1 Main themes
A. life elsewhere in the universe is likely to be microbial.
B. microbes are known to exist on other planets.
C. all extraterrestrials known are microbial.
A. Decomposition of dead matter and wastes
B. Digestion of complex carbohydrates in animal diets
C. Formation of greenhouse gases, CO2 and methane
A. cells with a true nucleus
B. the last universal common ancestor
C. photosynthetic bacteria
A. Bacteria in the soil secreting an antibiotic to kill competitors
B. Public health officials monitoring diseases in a community
C. Egyptians using moldy bread on wounds
D. A microbiologist using the microscope to view bacteria
C. Treating water and sewage
B. malaria and other protozoan diseases
D. measles and other rash diseases
A. Contain a nucleus to hold DNA
B. Contain ribosomes for protein synthesis
C. Contain membrane-bound organelles
A. Have a cell wall for rigidity
B. Can use flagella for movement
C. Contain mitochondria for energy production
A. Cannot be seen without a microscope
B. Contain genetic material
A. the decomposers in ecosystems
C. always harmful to their host
A. Viruses are smaller than eukaryotic cells, but larger than bacterial or archaeal cells.
B. Viruses are smaller than macromolecules.
C. Viruses are larger than eukaryotic cells.
A. Francesco Redi: tested spontaneous generation with meat exposed to the air or covered with cloth
B. Louis Pasteur: demonstrated that anthrax was caused by a bacterium
C. Joseph Lister: promoted disinfecting hands and air prior to surgery
A. The shape of the glass neck allowed the bacteria into the flask and then into the media, but air could not enter.
B. The glass necks needed to be open to the air, yet constructed so that bacteria would settle in the lowest part of the neck.
What are the Branches of Microbiology?
Microbiology can be divided into two branches: pure and applied. The former is the most fundamental branch, in which organisms themselves are examined in-depth. In applied microbiology, the organisms themselves are not studied but are applied to a certain process. Additionally, microbiology can be separated by taxonomy, which classifies different microbes (bacteriology, protozoology, etc.). Below are examples of each branch and taxonomy:
- Microbial Genetics – Studying the genetics within microorganisms, including bacteria, viruses and fungi, is the principal focus of microbial genetics. The examination of their growth rates and generation cycles helps scientists better understand a microorganism’s evolution.
- Immunology – Concentrating on the study of an organism’s immune system is the specialty of immunology. Scientists conduct research on the immune system to treat disorders within it, including autoimmune diseases, transplant rejection and hypersensitivities.
- Medical Microbiology – Focusing on the application of medicine, medical microbiologists diagnosis, treat and prevent infectious diseases. Additionally, these scientists study microbes to enhance overall health in humans.
- Biotechnology – Investigating methods of using living organisms to invent or produce products is the specialty of a biotechnologist. By using genetic engineering, along with cell and tissue technologies, physicians can customize treatments for their patients.
- Bacteriology – Researching methods related to producing medicine from bacteria is the study of bacteriology.
The UF master’s degree program offers courses that cover both pure and applied microbiology, providing a comprehensive understanding of this field. Additionally, our program incorporates courses from the College of Medicine that will provide a concentration in medical microbiology and biochemistry, offering you a unique educational experience unmatched by other programs. Other courses that will enhance your knowledge include:
Immunization, Antiseptics, and Antibiotics
Understanding microbes gives us the ability to fight pathogens using immunization, antiseptics, and antibiotics.
Compare immunization, antiseptics and antibiotics, and how they are used to combat human pathogens
- Immunization is the fortification of our own immune system, priming it against potential future infections by specific microbes.
- Antiseptics are broadly defined as substances we can use on our body or surfaces around us to slow or kill microbes that could potentially harm us.
- Antibiotics, like antiseptics, can slow or kill microbes. However, unlike antiseptics, antibiotics can circulate in the human blood system and be used to fight microbial infections.
- anaphylactic shock: A severe and rapid systemic allergic reaction to an allergen, constricting the trachea and preventing breathing.
- immunogen: any substance that elicits a immune response an antigen
Surprisingly, most microbes are not harmful to humans. In fact, they are all around us and even a part of us. However, some microbes are human pathogens to combat these, we use immunization, antiseptics, and antibiotics.
Immunization is the process by which an individual’s immune system becomes fortified against an agent (known as the immunogen ).
Flu Immunization: A naval officer self-administers a nasal spray that immunizes him against the flu.
When the immune system is exposed to molecules that are foreign to the body, it will orchestrate an immune response. It will also develop the ability to respond quickly to subsequent encounters with the same substance, a phenomenon known as immunological memory. Therefore, by exposing a person to an immunogen in a controlled way, the body can learn to protect itself: this is called active immunization.
Vaccines against microorganisms that cause diseases can prepare the body’s immune system, thus helping it fight or prevent an infection. The most important elements of the immune system that are improved by immunization are the T cells, the B cells, and the antibodies B cells produce. Memory B cells and memory T cells are responsible for the swift response to a second encounter with a foreign molecule. Through the use of immunizations, some infections and diseases have been almost completely eradicated throughout the United States and the world. For example, polio was eliminated in the U.S. in 1979. Active immunization and vaccination has been named one of the “Ten Great Public Health Achievements in the 20 th Century. ”
By contrast, in passive immunization, pre-synthesized elements of the immune system are transferred to a human body so it does not need to produce these elements itself. Currently, antibodies can be used for passive immunization. This method of immunization starts to work very quickly however, it is short-lasting because the antibodies are naturally broken down and will disappear altogether if there are no B cells to produce more of them. Passive immunization occurs physiologically, when antibodies are transferred from mother to fetus during pregnancy, to protect the fetus before and shortly after birth. The antibodies can be produced in animals, called ” serum therapy,” although there is a high chance of anaphylactic shock because of immunity against animal serum itself. Thus, humanized antibodies produced in vitro by cell culture are used instead if available.
In early inquiries before there was an understanding of microbes, much emphasis was given to the prevention of putrefaction. Procedures were carried out to determine the amount of agent that needed to be added to a given solution in order to prevent the development of pus and putrefaction. However, due to a lack of understanding of germ theory, this method was inaccurate. Today, an antiseptic is judged by its effect on pure cultures of a defined microbe or on their vegetative and spore forms.
Antiseptics are antimicrobial substances that are applied to living tissue to reduce the possibility of infection, sepsis, or putrefaction. Their earliest known systematic use was in the ancient practice of embalming the dead. Antiseptics are generally distinguished from antibiotics by the latter’s ability to be transported through the lymphatic system to destroy bacteria within the body, and from disinfectants, which destroy microorganisms found on non-living objects. Some antiseptics are true germicides, capable of destroying microbes (bacteriocidal), while others are bacteriostatic and only prevent or inhibit bacterial growth. Microbicides that destroy virus particles are called viricides or antivirals.
Antibiotic Testing: Discs soaked with various compounds are put onto a lawn of bacteria. If the compound on the disc kills or slows bacteria growth, a “halo” of clear media is seen.
An antibacterial is a compound or substance that kills or slows down the growth of bacteria. The term is often used synonymously with the term antibiotic today, however, with increased knowledge of the causative agents of various infectious diseases, the term “antibiotic” has come to denote a broader range of antimicrobial compounds, including anti-fungal and other compounds.
The word “antibiotic” was first used in 1942 by Selman Waksman and his collaborators to describe any substance produced by a microorganism that is antagonistic to the growth of other microorganisms in high dilution. This definition excluded substances that kill bacteria but are not produced by microorganisms (such as gastric juices and hydrogen peroxide). It also excluded synthetic antibacterial compounds, such as the sulfonamides. Many antibacterial compounds are relatively small molecules with a molecular weight of less than 2000 amu. With advances in medicinal chemistry, most of today’s antibacterials are semisynthetic modifications of various natural compounds.
Prokaryotes VS Eukaryotes
Defined as pre-nucleus, prokaryotes are cells that contain no membrane-based organelles, including a nucleus.
Mostly recognized as bacteria, two prokaryotic kingdoms exist: Monera or Bacteria and Archaea.
Seemingly simple in structure and markedly different from eukaryote and protist organisms, many scientists believe prokaryotic cells were amongst the first on the Earth and very well may out-survive all other organisms.
Prokaryotes are, with few exceptions, unicellular organisms many bacteria live in colonies, making them appear larger at first glance, but individual cells are visible under a microscope.
These cells do not possess membrane-based organelles, but the fundamentals of cell theory still apply.
Initially proposed by German scientists Matthias Schleiden and Theodor Schwann, and later amended by Rudolf Virchow, four basic rules apply to eukaryotic, prokaryotic and protist cells:
- All functions that make life possible occur within the boundaries of cells
- All cells possess genetic material required to regulate cell functions and replicate, passing this genetic information to new cells
Scientists have expanded and refined cell theory with the advent of advanced microscopy instruments, but these basic rules still apply to all cells.
Prokaryotes vs. Eukaryotes – Similarities?
All cells require energy to survive and undergo chemical processes to sustain life.
Biochemical processes often involve the use of carbohydrates, proteins, lipids and nucleic acids for cell functions such as:
- Obtaining food
- Turning food into usable energy
- Cell growth
- Cell replication
Elemental processes essential to the life – acquisition of energy, reproduction – are similar in prokaryotic and eukaryotic cells, regardless of the difference in structure and means.
Prokaryotes vs. Eukaryotes – Differences
Eukaryotes as well as protists, a miscellany group made up of eukaryote-like plant, animal and fungi missing one or more characteristics to be defined as purely eukaryotic, differ greatly from prokaryotes in structure.
Most significant is the lack of a nucleus in prokaryotic cells as well as membrane-based organelles found in all eukaryotic cells.
Both have DNA, but eukaryote-DNA contain histones and chromosomes in a linear structure.
Mitochondria (or the plant equivalent chloroplasts) is one of the many membrane-bound organelles present in eukaryotes, along with:
In addition, while eukaryotes can be uni- or multi- cellular, heterotroph or autotroph, prokaryotes are heterotrophic single-celled organisms.
The Prokaryotic Cell
Ranging from two to five micrometers (um), typical prokaryotic cell structure includes:
- Cell Wall – lends to the shape of the cell two types are gram positive and gram negative
- – hair-like projections surrounding the outer layer of the cell enables bacteria to stick-on surfaces or latch-on other cells
- Capsule – thick covering of the cell wall that can provide protection from phagocytosis, chemicals and dehydration the sticky nature allows it to adhere to other cells found in gram-positive bacteria and blue-green algae
- – attached to the cell wall, usually described as “whip-like” most prokaryotes are in constant motion and only able to move forward and backward
- Plasma Membrane – a thin, flexible asymmetrical “sac” that essentially contains the cell serves as a passageway for anything that enters or leaves the cell such as nutrients and gases also holds the cytoplasm
- – can be compared, in terms of purpose, as carrying out similar functions to membrane-bound organelles contains enzymes for and carries out metabolism important to note that nothing within the cytoplasm is separated via membrane or well-defined sections, items are suspended in the semi-fluid gel
- Nucleoid or Nuclear Body – area of the cytoplasm where the DNA strand is located
- – tiny rings of DNA that can be transferred to other cells anti-biotic resistance is a prime illustration of the way prokaryotes share information with other prokaryote cells, enabling cells to make adjustments that ensure survival
- – combination of RNA and protein, the function of prokaryotic ribosomes widely depends on the bacteria
Prokaryotes consist of two Kingdoms: Monera or Bacteria (sometimes called eubacteria), which includes cyanobacteria noted for the ability to carry out photosynthesis, and Archaea (archaebacteria).
With the greatest ability to withstand the most severe environmental conditions, science believes the latter contains the oldest cells/organisms on the planet, and sometimes referring to it as “ancient bacteria.”
The study of prokaryotic cells involves the study of bacteria – single cells that can be as tiny as two microns and look like dots under a compound microscope.
Bacteria are fascinating subjects for many reasons:
· Range of purpose – without the existences of many “good” bacteria, many species could not exist, including humans
· Are found everywhere – bacteria are not limited to causing disease, for example, they:
- Line human intestines to help with digestion
- Aid in the digestive process of rudiment animals
- Help decompose waste material
· Adaptability – some bacteria create endospores, enabling them to survive if placed in a different or “harsh” environment
· Can survive conditions that would kill other cells – for example, some live in exceptionally hot or cold temperatures, gaseous environments or in places with intense high or low Ph
· Function – even though the cell structure seems simple, especially when compared to eukaryotes, unicellular bacteria and archaea organisms not only perform complex functions to survive, they are the oldest known cells
· Colonization – many bacteria grow in colonies, yet each cell maintains its autonomy
· Reproduction – cells pass along genetic information via a process called binary fission cells create duplicate DNA and divide
Prokaryotes are classified through characteristics such as shape, behavior, size, growth, and stains.
Bacteria are separated into three classes based on shape: cocci, bacilli, and spirilla. Although defined by morphology, they might not fall into the same classification – the only commonality might be shape.
Also important to note, due to the size of bacteria, shapes are the only aspects visible under a light microscopes, such as electron microscopes, which offer more powerful magnification, in order to see the internal structures of the cell.
- Cocci are described as round, flat spheres and can be observed as lone cells, pairs, chains, tetrads (4 cells), clusters or cubes (8 cells) streptococcus is a chain of cocci-shaped bacteria cells responsible for the common sore throat infection
- Rods, sometimes described as cylindrical and called as bacilli exist as singles, pairs and chains unlike the simpler cocci, the length of chains has no bearing on identification , known for their spiral shape can appear as one curve, like elbow-macaroni, twists or genuine spirals
The way bacteria behaves is also important in identification attributes include:
- Whether a culture grows in a warm or cold environment
- Whether cells colonize
- DNA tests
- Cell behavior when exposed to a variety of filters, chemicals, elements, gases or states (i.e., dehydration, change in Ph)
- Growth (i.e., observing sample in a Petri-dish over time, possibly changing the external conditions)
In addition, bacteria are separated into gram positive and gram negative, easily discerned from one another by the use of a stain.
Prokaryote cells are especially intriguing to individuals interested in microbiology and microscopy.
Although shapes can be discerned under a compound microscope , powerful electron microscopes are required to observe internal details of the cell. Separated into Kingdoms Monera and Archaea, prokaryotes consist primarily of bacteria cells.
Ranging from 2-5 um, these impressive one-celled organisms survived millions of years notorious for the result of diseases, most eukaryotic organisms could not exist without “good” bacteria – including humans.
Using microscopy, researchers try to understand their ability to adapt and survive, the way they help the human body and how to use them to improve the earth.
To Read further about Eukaryotes, Cell Division and Cell Differentiation and more about Unicellular Organisms - discussing further about Bacteria, Fungi, Algae and Archaea .
The Prokaryotes is a comprehensive, multi-authored, peer reviewed reference work on Bacteria and Achaea. This fourth edition of The Prokaryotes is organized to cover all taxonomic diversity, using the family level to delineate chapters.
Different from other resources, this new Springer product includes not only taxonomy, but also prokaryotic biology and technology of taxa in a broad context. Technological aspects highlight the usefulness of prokaryotes in processes and products, including biocontrol agents and as genetics tools.
The content of the expanded fourth edition is divided into two parts: Part 1 contains review chapters dealing with the most important general concepts in molecular, applied and general prokaryote biology Part 2 describes the known properties of specific taxonomic groups.
Two completely new sections have been added to Part 1: bacterial communities and human bacteriology. The bacterial communities section reflects the growing realization that studies on pure cultures of bacteria have led to an incomplete picture of the microbial world for two fundamental reasons: the vast majority of bacteria in soil, water and associated with biological tissues are currently not culturable, and that an understanding of microbial ecology requires knowledge on how different bacterial species interact with each other in their natural environment. The new section on human microbiology deals with bacteria associated with healthy humans and bacterial pathogenesis. Each of the major human diseases caused by bacteria is reviewed, from identifying the pathogens by classical clinical and non-culturing techniques to the biochemical mechanisms of the disease process.
The 4th edition of The Prokaryotes is the most complete resource on the biology of prokaryotes.
The following volumes are published consecutively within the 4th Edition:
Prokaryotic Biology and Symbiotic Associations
Prokaryotic Communities and Ecophysiology
Prokaryotic Physiology and Biochemistry
Applied Bacteriology and Biotechnology
Alphaproteobacteria and Betaproteobacteria
Deltaproteobacteria and Epsilonproteobacteria
Other Major Lineages of Bacteria and the Archaea
Eugene Rosenberg, Professor of Microbiology at Tel Aviv University, Israel Edward F. DeLong, Professor at Department of Civil and Environmental Engineering & Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA Fabiano Thompson, Professor at Center of Health Sciences, Federal University of Rio de Janeiro, Brazil Stephen Lory, Professor at Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA, USA Erko Stackebrandt, Director of the German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
The ISME Journal seeks to promote diverse and integrated areas of microbial ecology spanning the breadth of microbial life, including bacteria, archaea, microbial eukaryotes, and viruses. Contributions of broad biological interest and impact are especially encouraged.
The central purpose of Microbiome is to unite investigators conducting microbiome research in environmental, agricultural, and biomedical arenas. Topics broadly addressing the study of microbial communities, such as, microbial surveys, bioinformatics, meta-omics approaches and community/host interaction modeling will be considered for publication.
The 5′ UTR begins at the transcription start site and ends one nucleotide (nt) before the initiation sequence (usually AUG) of the coding region. In prokaryotes, the length of the 5′ UTR tends to be 3–10 nucleotides long, while in eukaryotes it tends to be anywhere from 100 to several thousand nucleotides long.  For example, the ste11 transcript in Schizosaccharomyces pombe has a 2273 nucleotide 5′ UTR  while the lac operon in Escherichia coli only has seven nucleotides in its 5′ UTR.  The differing sizes are likely due to the complexity of the eukaryotic regulation which the 5′ UTR holds as well as the larger pre-initiation complex that must form to begin translation.
The 5′ UTR can also be completely missing, in the case of leaderless mRNAs. Ribosomes of all three domains of life accept and translate such mRNAs.  Such sequences are naturally found in all three domains of life. Humans have many pressure-related genes under a 2–3 nucleotide leader. Mammals also have other types of ultra-short leaders like the TISU sequence. 
The elements of a eukaryotic and prokaryotic 5′ UTR differ greatly. The prokaryotic 5′ UTR contains a ribosome binding site (RBS), also known as the Shine–Dalgarno sequence (AGGAGGU), which is usually 3–10 base pairs upstream from the initiation codon.  In contrast, the eukaryotic 5′ UTR contains the Kozak consensus sequence (ACCAUGG), which contains the initiation codon.  The eukaryotic 5′ UTR also contains cis-acting regulatory elements called upstream open reading frames (uORFs) and upstream AUGs (uAUGs) and termination codons, which have a great impact on the regulation of translation (see below). Unlike prokaryotes, 5′ UTRs can harbor introns in eukaryotes. In humans,
35% of all genes harbor introns within the 5′ UTR. 
Secondary structure Edit
As the 5′ UTR has high GC content, secondary structures often occur within it. Hairpin loops are one such secondary structure that can be located within the 5′ UTR. These secondary structures also impact the regulation of translation. 
In bacteria, the initiation of translation occurs when IF-3, along with the 30S ribosomal subunit, bind to the Shine–Dalgarno (SD) sequence of the 5′ UTR.  This then recruits many other proteins, such as the 50S ribosomal subunit, which allows for translation to begin. Each of these steps regulates the initiation of translation.
Initiation in Archaea is less understood. SD sequences are much rarer, and the initiation factors have more in common with eukaryotic ones. There is no homolog of bacterial IF3.  Some mRNAs are leaderless. 
In both domains, genes without Shine–Dalgarno sequences are also translated in a less understood manner. A requirement seems to be a lack of secondary structure near the initiation codon. 
Pre-initiation complex regulation Edit
The regulation of translation in eukaryotes is more complex than in prokaryotes. Initially, the eIF4F complex is recruited to the 5′ cap, which in turn recruits the ribosomal complex to the 5′ UTR. Both eIF4E and eIF4G bind the 5′ UTR, which limits the rate at which translational initiation can occur. However, this is not the only regulatory step of translation that involves the 5′ UTR.
RNA-binding proteins sometimes serve to prevent the pre-initiation complex from forming. An example is regulation of the msl2 gene. The protein SXL attaches to an intron segment located within the 5′ UTR segment of the primary transcript, which leads to the inclusion of the intron after processing.  This sequence allows the recruitment of proteins that bind simultaneously to both the 5′ and 3′ UTR, not allowing translation proteins to assemble. However, it has also been noted that SXL can also repress translation of RNAs that do not contain a poly(A) tail, or more generally, 3′ UTR.
Closed-loop regulation Edit
Another important regulator of translation is the interaction between 3′ UTR and the 5′ UTR.
The closed-loop structure inhibits translation. This has been observed in Xenopus laevis, in which eIF4E bound to the 5′ cap interacts with Maskin bound to CPEB on the 3′ UTR, creating translationally inactive transcripts. This translational inhibition is lifted once CPEB is phosphorylated, displacing the Maskin binding site, allowing for the polymerization of the PolyA tail, which can recruit the translational machinery by means of PABP.  However, it is important to note that this mechanism has been under great scrutiny. 
Ferritin regulation Edit
Iron levels in cells are maintained by translation regulation of many proteins involved in iron storage and metabolism. The 5′ UTR has the ability to form a hairpin loop secondary structure (known as the iron response element or IRE) that is recognized by iron-regulatory proteins (IRP1 and IRP2). In low levels of iron, the ORF of the target mRNA is blocked as a result of steric hindrance from the binding of IRP1 and IRP2 to the IRE. When iron is high, then the two iron-regulatory proteins do not bind as strongly and allow proteins to be expressed that have a role in iron concentration control. This function has gained some interest after it was revealed that the translation of amyloid precursor protein may be disrupted due to a single-nucleotide polymorphism to the IRE found in the 5′ UTR of its mRNA, leading to a spontaneous increased risk of Alzheimer's disease. 
UORFs and reinitiation Edit
Another form of translational regulation in eukaryotes comes from unique elements on the 5′ UTR called upstream open reading frames (uORF). These elements are fairly common, occurring in 35–49% of all human genes.  A uORF is a coding sequence located in the 5′ UTR located upstream of the coding sequences initiation site. These uORFs contain their own initiation codon, known as an upstream AUG (uAUG). This codon can be scanned for by ribosomes and then translated to create a product,  which can regulate the translation of the main protein coding sequence or other uORFs that may exist on the same transcript.
The translation of the protein within the main ORF after a uORF sequence has been translated is known as reinitiation.  The process of reinitiation is known to reduce the translation of the ORF protein. Control of protein regulation is determined by the distance between the uORF and the first codon in the main ORF.  A uORF has been found to increase reinitiation with the longer distance between its uAUG and the start codon of the main ORF, which indicates that the ribosome needs to reacquire translation factors before it can carry out translation of the main protein.  For example, ATF4 regulation is performed by two uORFs further upstream, named uORF1 and uORF2, which contain three amino acids and fifty-nine amino acids, respectively. The location of uORF2 overlaps with the ATF4 ORF. During normal conditions, the uORF1 is translated, and then translation of uORF2 occurs only after eIF2-TC has been reacquired. Translation of the uORF2 requires that the ribosomes pass by the ATF4 ORF, whose start codon is located within uORF2. This leads to its repression. However, during stress conditions, the 40S ribosome will bypass uORF2 because of a decrease in concentration of eIF2-TC, which means the ribosome does not acquire one in time to translate uORF2. Instead, ATF4 is translated. 
Other mechanisms Edit
In addition to reinitiation, uORFs contribute to translation initiation based on:
- The nucleotides of an uORF may code for a codon that leads to a highly structured mRNA, causing the ribosome to stall. 
- cis- and trans- regulation on translation of the main protein coding sequence. 
- Interactions with IRES sites. 
Internal ribosome entry sites and viruses Edit
Viral (as well as some eukaryotic) 5′ UTRs contain internal ribosome entry sites, which is a cap-independent method of translational activation. Instead of building up a complex at the 5′ cap, the IRES allows for direct binding of the ribosomal complexes to the transcript to begin translation.  The IRES enables the viral transcript to translate more efficiently due to the lack of needing a preinitation complex, allowing the virus to replicate quickly. 
Msl-2 transcript Edit
Transcription of the msl-2 transcript is regulated by multiple binding sites for fly Sxl at the 5′ UTR.  In particular, these poly-uracil sites are located close to a small intron that is spliced in males, but kept in females through splicing inhibition. This splicing inhibition is maintained by Sxl.  When present, Sxl will repress the translation of msl2 by increasing translation of a start codon located in a uORF in the 5′ UTR (see above for more information on uORFs). Also, Sxl outcompetes TIA-1 to a poly(U) region and prevents snRNP (a step in alternative splicing) recruitment to the 5′ splice site. 
5: The Eukaryotes of Microbiology - Biology
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Institute of Cell and Molecular Biology, The University of Edinburgh
This site was developed as a resource to support my teaching. All material is copyright of the author or other contributors BUT CAN BE USED FREELY FOR NON-PROFIT EDUCATIONAL PURPOSES. An acknowledgement would be appreciated.
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TO ENTER THIS SITE:
GO TO THE MICROBIAL WORLD (introduction to microorganisms, their activities and evolutionary relationships, including THE TREE OF LIFE )
OR: click on keywords on the globe >>
This is a clickable image
Microorganisms are everywhere - a largely unseen world of activities that helped to create the biosphere and that continue to support the life processes on earth. So, Welcome to the Microbial World. In fact, you are part of it!
Of all the cells that make up the normal, healthy human body, more than 99 per cent are the cells of microorganisms living on the skin or in the gut, etc. This normal resident microbial population includes potential pathogens as well as organisms that help to keep the potential pathogens in check (see Yeasts and yeast-like fungi ).
Here are a few more examples of the impact of microorganisms.
- Look at the scene below - part of the Lower Sonoran desert of Arizona. Every one of these plants depends on microorganisms. Microbes play a vital role in creating desert soils (see Cyanobacteria ). All of these plants have mycorrhizal fungi in their roots, serving for mineral nutrient uptake and probably also for water uptake (see Mycorrhizas ). The large feather-like bush (paloverde) to the right of the giant saguaro cactus is a member of the Leguminosae, with nitrogen-fixing Rhizobium in its root nodules (see Nitrogen fixation ). These plants, in turn, create the environment for desert animals - the kangaroo rat, cactus wren, Harris' hawk, Gila woodpecker, coyote, etc. [If you want to know more about desert environments and desert organisms, visit our Desert Ecology website ]
The main plants seen here are: the giant saguaro cactus (Carnegiea gigantea, about 6 metres tall), various species of Opuntia (large jointed pads of the prickly pear to the left and right of the saguaro, teddy bear cholla in the foreground, the purple coloured pencil cholla to the left of the saguaro), bursage (Ambrosia deltoidea) in much of the foreground, and paloverde (Parkinsonia), the green-stemmed tree to the right of the saguaro. [Image supplied by Sharon von Broembsen, Oklahoma State University]
- Microorganisms (including viruses) have major impact on human health (for example, see Airborne microbes Proteus ) and crop yields (for example, Biotrophs Vascular wilts ). But microorganisms also can be exploited to control disease, through production of antibiotics (see Penicillin ) or by acting as biological control agents (for example, see Heterobasidion Pythium oligandrum Agrobacterium ).
- Microorganisms are a major source of useful products, including pharmaceuticals (e.g. cyclosporins from fungi are used as immunosuppressants in transplant surgery), food supplements (see Xanthan ), and insecticidal compounds (see Bacillus thuringiensis ).
- Microorganisms have key environmental roles in regulating the populations of pest organisms (see Biological control , Catenaria ), in the cycling of mineral nutrients (see Winogradsky column Lichens ) and in decomposition of organic matter, including wood decay (see Armillaria mellea ) and the processing of human wastes (for example, Thermophilic microorganisms ). It is estimated that one-third of all the "fixed" nitrogen that supports plant (and therefore animal) growth on earth (nitrogen in the form of nitrates, ammonium compounds and amino acids, etc.) is lost to the atmosphere each year as a result of denitrification by microbial activities. But a similar amount of atmospheric nitrogen gas (N2) is fixed into plant-available forms each year by the many types of nitrogen-fixing bacteria . If these estimates are anywhere near correct, then microbes really do keep our world turning.
Our list could go on, but we end this section by noting the astonishing diversity of physiology and metabolism that enables microbes to grow in every environment that will support life on earth.
- We find fungi in environments too dry to support any other life form.
- We find archaea (see below) - growing at temperatures over 100 o C.
- Other archaea grow only in highly saline environments, where nothing else will grow.
- Some bacteria - the chemoautotrophs - grow in the simplest of all life-supporting conditions: they gain their energy by oxidising hydrogen or other inorganic substances, their nitrogen by fixing N2 gas, and all their carbon requirements from CO2.
Here we consider microorganisms in geological time - how they evolved and diversified, and how they created the world that we know today. We also see the place of microorganisms in the scheme of life as a whole, based on gene sequencing to analyse the relatedness of organisms.
An approximate history of life on earth is shown in the table below, based on information in Encyclopaedia Britannica (1986). There may be more up-to-date information, but the major points would still apply.
The evidence is fragmentary, and is obtained from three major sources:
- the fossil record, consisting of the preserved remains of organisms themselves (of limited value for microorganisms)
- geological deposits that are believed to result from biological activities
- changes in the oxidation states of sediments (e.g. banded iron formation) indicating the progressive development of an oxygenic atmosphere.
Millions of years before present
Geological / fossil record
[abstracted from Encyclopaedia Britannica, 1986]
- There has been life on earth for much of the planet's history. It is difficult to say when life first evolved or arrived here, but microbial life has been present for at least 3,500 million years, and the earth itself was only formed about 4,600 million years ago, after which its surface would need to have cooled to physiological temperatures.
- The early organisms would have been anaerobes. There is no primary source of oxygen on the earth, and any oxygen formed in the photodissociation of water by UV rays (with escape of hydrogen from the earth's gravitational field) would have combined rapidly with reduced substances. The early organisms would havebeen heterotrophs, using the accumulated organic matter formed by photochemical reactions. In the absence of oxygen and microbes, organic compounds would have persisted wherever they were sheltered from irradiation.
- Organisms resembling today's cyanobacteria probably existed about 2,800 million years ago. These organisms perform oxygen-evolving photosynthesis, like the green plants of today. But any oxygen that they produced would combine rapidly with chemically reduced substances in rocks and waters, so free oxygen would not accumulate in the atmosphere. These cyanobacteria almost certainly were preceded by organisms that performed anaerobic (non-oxygen-evolving) photosynthesis, like today's purple and green sulphur bacteria (see Winogradsky column ).
- Eukaryotic organisms - those with a nucleus and with much larger cells than the bacteria or cyanobacteria - are found in rocks from about 1,400 million years ago, and perhaps occurred as early as 2,000 million years ago. It is assumed that they developed in an oxygenic atmosphere.
- From about 650 million years ago we find the first evidence of primitive multicellular organisms, and from about 400 million years we see the development of primitive land plants.
- There is strong evidence that fungi were associated with these primitive land plants, giving rise to the mycorrhizal associations typical of much of the world's vegetation today (see Mycorrhizas ).
Biologists have always striven to find a universal "tree of life" - a tree that reflects the natural, evolutionary relationships of living organisms and that, hopefully, extends back to the very origins of life.
Prokaryotes and eukaryotes
An important step along the path was the recognition that living organisms can be separated into two basic types: those with cells that contain a nucleus (the eukaryotes) and those that lack a nucleus (prokaryotes). Essentially, all the multicellular life forms are eukaryotes (with larger cells, containing organelles and a relatively large genome distributed between several chromosomes) whereas all bacteria and bacterium-like organisms are prokaryotes (with small cells, no internal membrane-bound organelles and a single circular chromosome). The geological record shows that organisms resembling today's prokaryotes have existed on earth for probably 3,500 million years, whereas eukaryotes have existed for perhaps only 1,500-2,000 million years.
In recent years biologists have tended to recognise five Kingdoms of organisms: the Monera (bacteria and bacterium-like organisms) representing prokaryotes, and plants, animals, fungi and protists (mainly unicellular nucleate organisms) representing eukaryotes.
The Five Kingdom approach is attractive in its simplicity, but has significant problems. One of these concerns the protists - a wide range of disparate organisms such as amoebae, slime moulds, ciliates, algae, etc. that are grouped together as a kingdom with little justification. Another problem stems from the recognition in the 1980s that some bacterium-like organisms (first given the name archaebacteria, and now called archaea) are so different from the true bacteria that they can be separated as a group. They are prokaryotes, and they look like bacteria, but in terms of cellular biochemistry and genetics the archaea differ from both eukaryotes and bacteria (see below).
DNA sequencing has provided a new approach for studying evolutionary relationships, since:
1. all organisms have a genome,
2 . the genes that code for vital cellular functions are conserved to a remarkable degree through evolutionary time,
3. even these genes accumulate random changes with time (usually in the regions that are not vital for function). In this respect the gene changes are rather like the scars on a boxer's face - a record of the accumulated impact of time.
So, by comparing the genes that code for vital functions of all living organisms, it should be possible to assess the relatedness of different organisms. The gene most commonly used for this codes for the RNA in the small subunit (SSU) of the ribosome. [Ribosomes are the structures on which proteins are synthesised]. Some regions of this SSU rRNA (also termed 16S rRNA) are highly conserved in all organisms, whereas other regions are more variable.
By comparing the DNA sequences for 16S rRNA, Woese and his colleagues constructed a proposed universal phylogenetic tree, shown in simplified form below.
Proposed universal phylogenetic tree, based on nucleotide sequence comparisons of the DNA coding for the RNA of the small ribosomal subunit of different organisms. Only some of the microbial groups are shown here. [Based on a diagram in R Woese (1994) Microbiological Reviews 58, 1-9.]
The proposed universal phylogenetic tree recognises three Domains of organisms (Bacteria, Archaea and Eucarya) above the traditional level of Kingdoms. These domains seem to have diverged from one another a long time ago, presumably from an extinct or as yet undiscovered ancestral line. As shown in the diagram above, the archaea and eucarya seem to have arisen from a common line more recently than the divergence of these two groups from the bacteria. However, we should note that this tree is only provisional - it can look quite different if it is rooted by other methods. There will be many changes before we arrive at a universally acceptable tree, if ever!
For further details and discussion, see:
DM Williams & TM Embley (1996). Annual Review of Ecology and Systematics 27, 569-595.
The Tree of Life Project (not on this server)
What should we now recognise as Kingdoms? Perhaps all the terminal branches of the tree represent kingdoms or taxa of similar major rank, and more will be added as the sequences of other organisms become available. Clearly, some of these kingdoms (or potential kingdoms) have advanced and expanded much more than others - the plants, animals and fungi are major groups of organisms with distinctive lifestyles, whereas the slime moulds and ciliates, for example, have not expanded to the same degree.
Origin and evolution of eukaryotes
Eukaryotes must have arisen from prokaryotic ancestors. Many aspects of this are still unknown, but there is persuasive evidence that the mitochondria and plastids (chloroplasts) of todays eukaryotes are derived from prokaryotes. For example, both mitochondria and plastids have a single circle of DNA (the vestige of a bacterial chromosome) which codes for some of their functions. Also, mitochondria and plastids have ribosomes that resemble those of prokaryotes (termed 70S ribosomes) and that are sensitive to antibacterial antibiotics. Gene sequencing shows that:
- the mitochondrial genome almost certainly arose from a purple bacterium (see the tree above)
- the plastid genome almost certainly arose from a cyanobacterium.
Thus, it is believed that these organelles of eukaryotes represent bacteria that once lived inside the cells of other bacteria. Over evolutionary time, the endosymbionts (ntermal dwellers) lost the ability for an independent life and became reduced to the state of serving particular functions (oxidative energy metabolism, and photosynthesis) in eukaryotes.
It is much more difficult to trace the origins of two other characteristic features of eukaryotes - the nucleus and the cytoskeleton (which is composed or microtubules and associated proteins).
Genealogies based on the genes coding for small subunit ribosomal RNA (as in the diagram above) provide a rather simple view of an ordered sequence of evolutionary progression. However, the situation becomes more complex when these findings are supplemented with the DNA sequence data for other genes, such as those encoding important enzyme functions. Then it becomes clear that the genomes of eukaryotes are chimeric - they have some gene sequences that clearly resemble those of the archaea and some that resemble those of bacteria. In other words, there does not seem to be an ordered, linear sequence of genetic change during the early evolution of the major groups of eukaryotes. Instead, there is likely to have been one or more gene transfer events between the evolving lines of bacteria, archaea and eucarya. One way in which this could have happened is by engulfment of one organism by another (perhaps followed by endosymbiosis), then some of the engulfed organism's genes might have been retained while others were lost over time.
For further discussion of all these points, see:
Symposia of the Society for General Microbiology Volume 54. Evolution of Microbial Life (1996) Cambridge University Press.
Laura A Katz (1998) Changing perspectives on the origin of eukaryotes. Trends in Ecology and Evolution Volume 13, 493-497.
The archaea are a fascinating group of organisms. Although they look like bacteria, and have simple cells with a prokaryotic structure, they have biochemical and genetic features quite different from those of bacteria. For example:
- they do not have peptidoglycan in their walls
- at least some of them have sterols in the cell membrane (a feature of eukaryotes),
- and they have different membrane lipids from those of either eukaroytes or bacteria (including ether linkages rather than ester linkages).
In terms of physiology and behaviour, the archaea fall into three major types.
- Extreme thermophiles, growing at temperatures of 80 o C or more. These organisms typically occur near geothermal vents (see Thermophilic microorganisms ).
- Halophiles, growing in extremely saline environments - they require solutions of at least 10% sodium chloride for their growth.
- Methanogens (methane-generators), which grow in anaerobic conditions, gaining energy by oxidising hydrogen. For this, they use CO2 as the oxidant, reducing it to methane (CH4) in the process. The methanogens use simple organic acids such as acetate for synthesis of their cellular components. These organic acids are produced by other anaerobic bacteria as the end-products of growth on cellulose and other polymers. So, the methanogens are abundant wherever organic matter is present in anaerobic conditions - land-fill sites, the rumen of cows, etc.
The growth conditions for the archaea are thought to resemble those that existed in the early stages of the earth's history. Thus, these organisms were termed archaebacteria (ancient bacteria) when they were first discovered. But we should not assume that they were necessarily the first microorganisms.
Newly discovered microbes
We have always known that the current methods of sampling and culturing of organisms from natural environments are deficient - these methods tend to select for the fastest-growing organisms in the culture conditions that are used. But the DNA sequencing methods discussed earlier have been a powerful new tool for detecting and ultimately isolating unknown (and even unsuspected) microorganisms.
Basically, DNA is extracted from an environmental sample, split into single strands and mixed with a primer - a short DNA sequence that will combine with the complementary sequence on DNA in the sample. Then by the polymerase chain reaction the DNA in the environmental sample will be synthesised, starting at the primer and copying along the DNA strand. By using a primer from a highly conserved region of the gene for SSU rRNA, any ribosomal genes in the sample will be copied and their sequences can be compared with the sequences of known organisms. Any new gene sequences will represent new organisms, and these can be placed within the SSU rRNA gene tree.
I n this way, two new types of archaea have been discovered from marine environments in the last decade. They seem to be remarkably common around the world, and the abundance of their DNA in coastal surface waters suggests that they can represent about 34% of the prokaryote biomass at certain times of the year.
See: DM Williams & TM Embley (1996). Annual Review of Ecology and Systematics 27, 569-595.
For more on the archaea and molecular evolution, some good starting points are:
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Eukaryote, any cell or organism that possesses a clearly defined nucleus. The eukaryotic cell has a nuclear membrane that surrounds the nucleus, in which the well-defined chromosomes (bodies containing the hereditary material) are located. Eukaryotic cells also contain organelles, including mitochondria (cellular energy exchangers), a Golgi apparatus (secretory device), an endoplasmic reticulum (a canal-like system of membranes within the cell), and lysosomes (digestive apparatus within many cell types). There are several exceptions to this, however for example, the absence of mitochondria and a nucleus in red blood cells and the lack of mitochondria in the oxymonad Monocercomonoides species.
Eukaryotes are thought to have evolved between about 1.7 billion and 1.9 billion years ago. The earliest known microfossils resembling eukaryotic organisms date to approximately 1.8 billion years ago. Compare prokaryote.
The Editors of Encyclopaedia Britannica This article was most recently revised and updated by Kara Rogers, Senior Editor.