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EVIDENCE FOR EVOLUTION FROM CELL MEMBRANE PROTEINS

 

HOMOLOGIES ARE PREDICTED BY THE EVOLUTIONARY MODEL

     The proteins involved in cell division and other cellular processes to not have to possess any specific form.  Although modern animal cells use the reversible phosphorylation of certain amino acids as the signal which determines whether these proteins are “on” or “off”, many other changes could conceivably bring about the same result.  For example, a change in a protein’s state could conceivably be signaled by the addition of some amino acids, the removal of amino acids, the modification of an amino acid to an unusual form, the modification of protein shape, or the addition of a variety of functional groups to amino acids such as methyl groups, oligosaccharides, lipids, etc.  Some of these mechanisms are used by living cells in molecular pathways.

     In the same way, there are many potential protein pathways which could control cell division.  There are a potentially endless number of conceivable proteins which could signal each other, inhibit each other, etc.  No one set is required  in order for cells to control their cell division.  When comparing signaling molecules within one organism or between organisms, there is no pattern which would be expected if evolution had not occurred.  The molecular evidence does not support this model.  Analysis of the proteins used in a single organism to control cell division and other processes and those of different organisms identifies homologous groups of genes predicted in the evolutionary model. 

 

1) HOMOLOGIES IN GENE FAMILIES

     Not only has genetic analysis demonstrated that the existence of gene families of cell division and signaling proteins composed of modified duplications of ancestral genes, the analysis indicates at what points in vertebrate history the duplications occurred. 

     There is no reason that gene families have to exist in the human genome: each gene could be a unique entity with a unique structure and separate origin.  This uniqueness is not observed.  Genomes of complex organisms seem to owe much of their gene content to the duplications of a smaller set of ancestral gene present in simpler ancestral organisms.  Some of these gene families contain members which perform similar roles such as the cyclin gene family which regulates the progression of the cell cycle through its various phases.  There is no reason that the cyclins need be homologous proteins of the same gene family, however.  This concept is even more obvious when the members of the gene family perform different functions as in the following examples from the human genome.  Human cells could conceivably perform all of the following functions with proteins which are not homologous members of the same gene family.

--The protein p53 is perhaps the most important tumor suppressor protein in human cells and its mutation is responsible for more human cancers than any other single cause.  The two human homologs of p53, p63 and p73, are involved in development, immunity, and neurogenesis.  p63 helps to maintain the epithelial lining and is required for proper development of the skin, limbs, breast, and prostate.  p73 functions in the development of neurons, inflammation, and pheromone detection. 

--The retinoblastoma (RB) tumor suppressor protein is homologous to the cyclins and TFIIB, which are not tumor suppressors. 

--Ankyrin gene family members interact with a variety of proteins, such as spectrin in the cytoskeleton, ion channels, ion pumps, and cell adhesion molecules.   Some ankyrin family members function in the nucleus, some are attached to the cell membrane (such as notch) and others are secreted (Kohl, 2003).  One of the new domains which evolved in the first animals was an apoptosis-promoting death domain, which was derived from ankyrin-like domains.  Death domains are part of the ankyrin family and include the caspases which can cause programmed cell death (Muller, 2001a; Wiens, 2000). 

--Related phosphatases can mediate a variety of cellular processes.  For example, PTPRC is a major molecule on the surface of leukocytes where it may comprise 10% of the cell surface.  It regulates proliferation, antiviral responses, and erythropoeitin response.  Mutations cause SCID and multiple sclerosis. (A lymphocyte is pictured below.) PTPRD is expressed in hippocampal regions CA2 and CA3, on B lymphocytes, and the thymus.  Mutations in mice result in learning deficits.  PTPRN only has one phosphatase domain (unlike most family members) and is expressed in the brain, pituitary, and pancreas.  It is an autoantigen in IDDM diabetes.

--Related kinases can mediate a variety of distinct reactions.  For example, Mos is a MAP3K kinase which functions in vertebrate and invertebrate oocytes to regulate the second meiotic division and to prevent mitosis until after fertilization (Tachibana, 2000).  MAP2K4 is induced by Ras and growth receptors.  In mice, null mutations cause death in embryonic development.  C. elegans possesses homologous enzymes which function in resistance to microbes; plants use homologues for pathogen resistance.  MAPK3 is expressed in the developing thymus and is involved in the plasticity of the developing visual cortex and other brain regions.  MAPK4 mutations in mice cause death in fetuses due to problems with blood vessel and heart development. 

--Different dual specificity tyrosine-phosphorylation-regulating kinases also vary in their functions.  DYRK1A is expressed in the frontal lobe and affects neural function in mice.  It is a candidate for causing some of the mental deficits in Downs syndrome.  DYRK2 and DYRK3 are highly expressed in the testis after the onset of spermatogenesis. 

--ERBB2 can be involved in several human cancers including breast and prostate cancer.  Increased expression causes resistance to taxol and thus chemoresistance in cancer patients.  One polymorphism (Val655to ile) increases the risk of breast cancer.  African populations have a lower frequency of this allele and thus a lower risk of breast cancer.  In contrast, ERBB4 functions in cell proliferation, differentiation, and synapse formation. 

--Receptors for fibroblast growth factor are kinase enzymes which also vary in their functions.  FGFR1 mutations cause skeletal disorders, cancer, Pfeiffer syndrome and Kallman syndrome (which may include cleft palate, multiple dental agenisis, an absence of the corpus callosam, fusion of the fourth and fifth metacarpals, and hearing loss).  FGFR2 mutations cause Crouzon Syndrome, Jackson-Weiss Syndrome, Pfeiffer Syndrome, Apert Syndrome, Beare-Stevenson Syndrome, Cutis Gyrata Syndrome, and craniosyntosis (OMIM).  Mutations in FGF receptor proteins 2 aqnd 3 can cause syndactyly of hands and feet; brachdactyly, finger-like thumbs, triphalangeal thumbs, fusion of ankle and wrist, and tibial curvature, among other changes (Manouvrier-Hanu, 1999).  FGFR3 mutations affect cartilage development and endochondral bone and epiphyseal plates.  Mutations can also cause hyperpigmentation and some cancers.

--STK11 mutations cause Peutz Jeghers syndrome with abnormal melanocyates in the lips, mouth , and digits and an increased risk of tumors.  Mutations have been observed in testicular tumors, pancreatic cancer, and melanoma. STK12 suppresses cytokinesis and is associated with multinuclearity and polyploidy.  STK13 is homologus to Drosophila and yeast proteins which are involved in centromere and chromosome separation.  STK16 overexpression causes the Golgi to break up into vesicles; it may be involved in the formation of vesicles from the Golgi and secretion.  STK21 is expressed in keratinocytes, the brain, spleen, lungs and testis.  Mutant mice die of seizures and display high levels of apoptosis in the hippocampus and cerebellum and reduced numbers of neurons in the olfactory bulb.

--Kinases may have evolved from ABC cassette transporter proteins (Plowman, 1999). 

      The preceding examples of gene family members which perform diverse functions in the human body support the evolutionary model.  The human genome is not composed of tens of thousands of unique genes which are unrelated to all others.  Instead, the large numbers of human genes can be divided into gene families which resulted from duplication and subsequent modification of a smaller set of ancestral proteins.

 

2) HOMOLOGIES IN DISTANTLY RELATED ORGANISMS

     The genes and proteins of the human genome do not have to possess homologs within the human genome and they certainly do not have to be homologous to the genes of other organisms.  Human cell division could use genes which are entirely different from those found in unicellular yeast.  The genes which humans use to prevent cancer could be completely different from those found in nematode worms or fruit flies.  This is not the case, however.  Many of the human genes which regulate the cell cycle and other cellular processes are homologous to those found in other organisms.      

     All eukaryotes share a number of proteins which regulate the cell cycle, such as cyclins, kinases, phosphatases, growth factors, and their receptors.  Programmed cell death occurs in unicellular eukaryotes, even those which lack mitochondria (Chose, 2003).  Homologs of human apoptotic proteins are known in many unicellular organisms, even bacteria (Aravind, 2003 ; Chose, 2003).    Flies possess Apaf-1 homolog, seven caspases and 2 Bcl-2 proteins in addition to other apoptotic proteins which have homologs in mammals such as cytochrome c, HtrA2/Omi, AIF, and EndoG (Igaki, 2004).    Apoptotic pathways have been conserved in bilateran animals given that expression of the pro-apoptotic nematode protein CED-4 in the cells of flies causes apoptosis (Kanuka, 1999) and human Bcl-2 can prevent cell death in nematode cells (Vaux, 1993).

     Protein kinases compose 1-3% of the genes in eukaryotic genomes and are one of the largest families of enzymes of organisms as diverse as humans and yeast.  Protein tyrosine kinases are major signaling factors in metazoan animals and abnormal expression of these enzymes cause a number of human diseases.  The various subfamilies were expanded early in the evolution of vertebrates (Gu, 2003).  Most bacterial genomes seem to possess between one and ten serine/threonine kinase genes, which were formerly though to be unique to eukaryotes (Han, 2001).  “Eukaryotic” protein kinases in microbes include Pkn1, YpkA, Etk, Stk,Spk, and Mbk (Kenelly, 2002).  Most gram positive bacteria control their catabolic genes (which comprise about 10% of their genome) with the phosphorylation of serine residues as a catabolite corepressor using HPr kinase/phosphorylase (Mijakovic, 2002). 

     There is evidence that the receptor tyrosine kinases, once thought to be specific to animals, evolved in the unicellular ancestors of animals.  While receptor tyrosine kinases are known primarily in metazoan animals (such as the planarian pictured above) where they are involved in many essential signaling pathways involved in animal development, a receptor tyrosine kinase is known from the protistan group choanoflagellates.  A number of genetic studies have indicated that choanoflagellates are the closest protistan relatives of the metazoans, which is supported by their possession of important animal genes not known from any other eukaryotic group (King, 2001).

     There are a number of kinase signaling cascades which exist in both worms and humans such as the AGC group of kinases (homologous to AKT and PDK1 in mammals), CAMK group (including death associated protein kinases, MAPK-associated kinases, myosin light chain kinase, and phosphorylase kinase), CMGC group (including the cyclin depenednet kinases, GSK-3, MAPKs, and CLK), STE group (including homologs of mammalian RAF, MLK, and TAK1 genes), receptor tyrosine kinases (the largest group of kinsaes in all higher eukaryotes from worms to humans), and the protein-tyrosine kinase group.  The CAMK group of kinases is absent from yeast and help multicellular organisms reach greater complexity.  The RCK gene family (which includes seven genes in humans in addition to genes in worms) is also absent in yeast.  Worms and humans both have more than twice the number of MAP kinases known in yeast (Plowman, 1999). There are about 94 subfamilies of kinase enzymes which are only known from animals.  A number of kinase subfamilies are only known in coelomate animals (and not in C. elegans) such as Jak A, JakB, Syk, Tek, Slob, Ste20 NinaC, CCK4, Musk, Ret, PDGF/VEGFR, Sev, Lisk, Mos, TOPK, Trb, and CDK10 (Manning, 2002). 

       Animals rely on their circadian rhythms to properly time their sleep/awake cycle, mating seasons, migrations, hibernations, and other timed events.  Animal circadian rhythms utilize proteins which evolved long before animals.  Casein kinase II is involved in the response to ultraviolet light in eukaryotes from yeast to humans; it is also involved in circadian rhythms in diverse eukaryotes including plants, fungi, flies and mammals.  Not only is there a common ancestral mechanism involved in eukaryotic time-keeping, it may have evolved from mechanisms which functioned in the prevention of ultraviolet light damage (Lin, 2002).  Casein kinase II functions in cell cycle regulation in fungi and animals.  Human and worm proteins can substitute for the function of yeast proteins in yeast (Dotan, 2001). 

     The phosphatases of mammalian genomes are similar.  There is only one protein-tyrosine-phosphatase which is known in rodents which does not exist as functional gene in humans.  The rodent OST-PTP gene is homologous to a pseudogene in humans (Cousin, 2004). 

      Comparative genome analysis supports the conclusion that modern organisms share a common ancestry.  The kinase, phosphatase, and cell cycle genes in humans are modified versions of homologous proteins which exist in other organisms.

 

C) THE GENE CLADOGRAM AND “IRREDUCIBLE COMPLEXITY”

     One of the main arguments in “Intelligent Design” is that of “irreducible complexity.”  Advocates of Intelligent Design have argued that molecular systems in living organisms involve multiple interacting genes and that such complex pathways could not have evolved gradually.  Analysis of the distribution of kinase, phosphatase, cell cycle, and apoptotic genes strongly refutes this.  As the following gene cladogram illustrates, the components of molecular pathways do not appear all at once in complex pathways.  Instead, it is apparent that throughout evolution organisms incorporated proteins which their ancestors possessed into new roles which were elaborated over time.  The complex molecular systems found in humans are not irreducibly complex in that, while their multiple interacting parts may be required for human life, no such system is a requirement for life in general.  A much simpler set of molecular mechanisms were sufficient for simple, ancestral organisms.  Some of these organisms evolved new molecular pathways through the duplication and modification of existing genes, the shuffling of protein domains, mutation, etc.  At first these novelties would not have been essential for life, but rather supplementary systems which gave their bearers an advantage over other organisms.  The descendants of these organisms evolved in ways so that these molecular mechanisms were required to support greater molecular complexity.

      It does not appeared that complex, designed life appeared from nowhere.  For example, it is certainly possible that the proteins which control the division of the eukaryotic nucleus appeared from nowhere in ancestral eukaryotes.  The evidence does not support this however.  Some proteins which are involved in the initiation of the eukaryotic cell cycle may have homologs in bacteria, such as Cdc6/Cdc18, MCMs, and Cdc45 (Leatherwood, 1998).  The cyclins which regulate the eukaryotic cell cycle are homologous to transcription factors in archebacteria.  GTF2B is part of the TFIIB complex which is involved in transcription in eukaryotes, eubacteria, and archebacteria.  It is homologous to cyclin A, indicating that cyclins may have evolved from proteins with a more generalized role in transcription in the ancestors of eukaryotes (OMIM; Bagby, 1995). 

     All eukaryotes use multiple kinases to regulate the cell cycle.  Although the cyclin-dependent kinases perhaps the best known, they do not appear to have been the first kinases to regulate the cell cycle.  In comparing the subfamilies of kinases involved in the regulation of the cell cycle in higher and lower eukaryotes, it is evident that the duplication of ancestral kinase genes involved in the cell cycle occurred in the evolution of the earliest eukaryotes.  The earliest branch contains kinases which function as a checkpoint of the cycle, followed by branches containing other kinases which regulate mitosis and meiosis.  The CDK family seems to have been the last group to evolve (Krylov, 2003).

    Although multicellular organisms rely on the programmed death of certain cells in processes ranging from normal development to the prevention of cancer, many molecular mechanisms of this process evolved before multicellularity.  Programmed cell death occurs in unicellular eukaryotes, even those which lack mitochondria (Chose, 2003).  Some bacteria undergo death in culture in order to limit the spread of bacteriophage (Fraser, 1998). Homologs of apoptotic proteins are known in bacteria, such as homologs of caspases, TIR (Toll-interleukin-1 receptor),  AP-ATPases, HtrA2/Omi homolog (high temperature requirement protein A2), EndoG , and apoptosis-inducing factor (AIF)(Aravind, 2003 ; Chose, 2003).  Omi/HtrA2 is an apoptotic serine protease which is homologous to the bacterial endoprotease HtrA.  In bacteria, it functions in the folding and degradation of proteins.  In eukaryotic cells under normal conditions Omi/HtrA2 is contained in the mitochondria, but during apoptosis, it binds (and thus inactivates) the inhibitor of apoptosis proteins (IAPs).  The homology of mitochondrial HtrA-like proteases to bacterial enzymes supports the endosymbiotic origin of mitochondria (Lorenzo, 2004).  EndoG is a member of the magnesium-dependent nuclease enzymes.  It functions in the replication of mitochondrial DNA under normal conditions and in bacteria, it repairs DNA among other functions.  During apoptosis, it degrades nuclear DNA independent of caspases.  CAD (caspase-activated DNase) also performs this function as part of the caspase pathway (Lorenzo, 2004).  Bacteria possess homologs of caspases, TIR (Toll-interleukin-1 receptor), and AP-ATPases which eukaryotes use in apoptotic pathways (Aravind, 2003). 

      Many of the important apoptotic proteins possess a region known as the death domain.  One of the new domains which evolved in the first animals was a death domain, which was derived from ankyrin-like domains of more primitive eukaryotes. Death domains are part of the ankyrin family (Muller, 2001a; Wiens, 2000).  Caspases arose early in evolution and are known in bacteria. (Aravind, 2003).  During oogenesis in Hydra, nurse cells utilize both caspase dependent and caspase independent pathways in apoptosis (Technau, 2003).  

      The response of mitochondria to stress shares a number of characteristics with the formation of bacterial spores.  It appears that the early eukaryotes adapted the stress responses of endosymbiotic mitochondria to become the apopototic response to stress (Frank, 2003).  Programmed cell death might be a relic of the relationship between two separate genomes in the ancestral eukaryote (Ameisen, 2002).  Mitochondria release proteins which cause apoptosis through both caspase dependent and caspase-independent pathways.  Mitochondria store a variety of proteins which can be released to destroy the cell (Lorenzo, 2004).   

     Ancestral genomes seem to have created much of their diversity by “domain shuffling”—exchanging small functional protein domains from separate proteins and combining them in new ways.  The majority (if not all) of the domain shufflings which produced the various subfamilies of the protein tyrosine kinase gene family had occurred before the split of sponges and higher animals.  The same observation is true of other gene families such as protein tyrosine phosphatase and phosphodiesterase families (Suga, 2001). 

 

 

THE GENE CLADOGRAM

Many of the genes which humans require to be human evolved long before humans.  The distribution of these genes among modern organisms supports that modern groups of organisms can be organized into clades which share a common ancestry.  The same clades of organisms which are supported through the analysis of signaling molecules are supported by the analysis of other genes, anatomical features, embryological development, and the fossil record.  The organization of modern organism into a nested hierarchy of clades is predicted by the evolutionary model but not alternative models.

 

ALL LIFE

--The eukaryotic type of kinases do exist in some prokaryotes and seem to have preceded the evolution of the eukaryotes (Ogawara, 1999; Gallinier, 1998).   

--Bacteria use carbamoyl phosphate synthetase to generate ATP from ADP.  In eukaryotes, CPS functions in synthesizing carbaomoyl phosphate which is a precursor or arginine and pyrimidine bases.   A  CPS enzyme from archaea seems to be an intermediate between the two (Ramon-Maiques, 2000) .

--The low molecular tyrosine phoshatases in mammals are homologous to arsenate reductase which protect bacteria and yeast from the toxic compound arsenate (Bennet, 2001).

-- Some proteins which are involved in the initiation of the eukaryotic cell cycle may have homologs in bacteria, such as Cdc6/Cdc18, MCMs, and Cdc45 (Leatherwood, 1998; Huettenbrenner, 2003).

--Homologs of apoptotic proteins (such as HtrA2/Omi homolog high temperature requirement protein A2 and apoptosis-inducing factor AIF) are known in bacteria (Chose, 2003).

--Bacteria possess homologs of caspases, TIR (Toll-interleukin-1 receptor), and AP-ATPases which eukaryotes use in apoptotic pathways (Aravind, 2003). 

--The response of mitochondria to stress shares a number of characteristics with the formation of bacterial spores.  It appears that the early eukaryotes adapted the stress responses of endosymbiotic mitochondria to become the apopototic response to stress (Frank, 2003). 

--Some proteins which are involved in the initiation of the eukaryotic cell cycle may have homologs in bacteria, such as Cdc6/Cdc18, MCMs,Cdc45 (Leatherwood, 1998), and cyclins  (Noble, 1997).

 

EUKARYOTES

--Yeast possess more than 100 protein kinase genes, representing about 2% of their genome.  This includes members of the MAPK, MAP2K, MAP3K casein kinase I and II families and others including CDCactivated protein kinase and histidine kinases (homologs of the main group of kinases known from eubacteria).  While there are no receptor tyrosine kinases, there are a few kinases which can phosphorylate serine, threonine, and tyrosine (Hunter, 1997).

Of 120 kinase enzymes known in yeast, only 23 belong to yeast-specific gene subfamiles.  The others are members of subfamilies found in higher organisms (Manning, 2002).

--Plant receptor-like kinases (RLKs) possess a signal sequence, a transmembrane region, and a cytoplasminc kinase domain and function in diverse signaling pathways which include meristem development, leaf development, bacterial resistance, and self-incompatibility.  As of 2001, there are more than 9000 different RLKs and related kinases identified in plants.  RLKs form a gene family of serine/threonine/kinases which include the Pelle kinases in animals as part of their clade.  Drosophila and C. elegans possess one gene in the RLK family while humans possess three.  (Shiu, 2001). 

--While receptor tyrosine kinases are known primarily in metazoan animals where they are involved in many essential signaling pathways involved in animal development, a receptor tyrosine kinase is known from the protistan group choanoflagellates.  A number of genetic studies have indicated that choanoflagellates are the closest protistan relatives of the metazoans, which is supported by their possession of important animal genes not known from any other eukaryotic group (King, 2001).

--The MAPK family has 3 subgroups: the extracellular signal kinases (ERKs), the stress-activated protein kinases (SAPKs) and the MAP3K subgroup.  ERK subgroup members are known in plants, yeast, and animals; the SAPK subgroup members are known from animals and yeast; and the MAP3K subgroup is known from animals and protozoans (Kultz, 1998).

--Casein kinase II is involved in the response to ultraviolet light in eukaryotes from yeast to humans; it is also involved in circadian rhythms in diverse eukaryotes including plants, fungi, flies and mammals (Lin, 2002).

--PI3Ks are used in yeast, slime molds, plants, nematodes, fruit flies, and mammals  (Vanhaesebroek, 1997).

--The enzyme multiple inositol polyphosphate phosphatase (MIPP) removes the phosphates from these inositol polyphosphates which possess more than 4 phosphate groups.  These enzymes are known from both plants and animals (invertebrates and vertebrates) and form a distinct subfamily of histidine phosphatase enzymes (Chi, 1999).

--Plant and animal groups of protein phosphatases form separate groups, their branches having evolved after the split of animal and plant lineages  (Lin, 1999).

 --Wild type yeast will die when exposed to a number of environmental stresses, but this cell death can be prevented in transgenic yeast which express nematode ced-9 proteins, human bcl-2 proteins, or chicken bcl-xl proteins.  Thus it seems that the cellular machinery utilized by anti-apoptotic proteins in higher eukaryotes also exist in unicellular eukaryotes although they seem to lack the signals themselves.  In response to stress, yeast cells condense their chromatin, break their DNA molecules into fragments, and expose phosphatidylserine on their cell membrane.  The same processes occur in apoptotic animal cells.  A number of the proteins which animal cells use to induce apoptosis (Bax, caspases, p53, and CED4/Apaf-1) also kill yeast cells (Chen, 2003).

--CDC28/cdc2 at least since yeast (Takeo, 2004)

--All eukaryotes share checkpoints at the beginning of S and M (Takeo, 2004).

--All eukaryotes share checkpoints preceding the beginning of the S and M phases of the cell cycle (Takeo, 2004). 

--The G2-phase DNA-damage checkpoint is regulated by PI3K-like complexes (such as as ATM), checkpoint loading complexes (CLC), checkpoint sliding clamps (CSC), BRCT proteins (perhaps including BRCA) and effector kinases.  Yeast and human homologs of all these proteins exist  (O’Connell, 2000)

 

ANIMALS

--The majority (if not all) of the domain shufflings which produced the various subfamilies of the protein tyrosine kinases had occurred before the split of sponges and higher animals.  Similar conclusions from protein tyrosine phosphatase and phosphodiesterase families (Suga, 2001).  Non-receptor PTKs  members of the Src and Fes families in sponges and non-receptor PTKs  members of the Src and Fes families (Schacke, 1994b; Gamulin, 1997; Steele, 1999). 

Higher animals use the p38 pathway in  responses to stress and microbes, using SAPK2 (stress activated protein kinase), a member of the MAPK gene family.  Sponges possess a homolog (Bohm, 2000).

Ca/CaM-dependent protein kinase is a serine/threonine kinase.  A number of invertebrates, ranging from sponges through protostomes and primitive deuterostomes, possess a single CamM kinase II gene.  Most vertebrates posses four genes (Tombes, 2003). 

--Diverse creatine kinases (cytoplasmic, mitochondrial and flagellar) are known in both protostomes and deuterostomes. Some duplications occurred in this family before the separation of sponges from other animal lineages, given that sponges possess homologs of the flagellar and mitochondrial creatine kinases.   In vertebrates there are two cytoplasmic genes, one of which is primarily expressed in muscle, the other in nervous tissue.  The proteins can function in both homodimers and heterodimers (Sona, 2004).

--Sponges utilize apoptosis in the formation of gemmules and in responses to environmental stresses and use caspases in the rejection of allografts.  This indicates that apoptosis evolved early in the history of multicellular animals (Wiens, 2003). 

--Sponges do demonstrate apoptosis and incorporate the gene MA-3 gene which is also a protein used in apoptosis in mammals (Muller, W.E.G., from Muller, 1998.89)

--Sponges possess proteins which, when introduced into human cells, are capable of decreasing the amount cyclin B1, stop the cell cycle before M, and induce apoptosis.  Thus, some of the regulatory mechanisms involving cyclin B and cell cycle control evolved before the first animals (Brown, 2004).

 

METAZOANS

--Mammals have two Syk genes (Syk and  ZAP-70) whose major known function is signal transduction in immune reactions.  Syk is present in cnidarians where it interacts with surface receptors (Steele, 1999).

--During oogenesis in Hydra, nurse cells utilize both caspase dependent and caspase independent pathways in apoptosis (Technau, 2003). 

 

BILATERANS

 --C. elegans uses a number of pathways in its responses to pathogens including the p38 MAP kinase pathway, apoptotic pathways, TGF-β pathways, and DAF-2 insulin/IGF-I like pathway (Nicholas, 2004).  In C. elegans, apoptosis involving caspases and Bcl-2 funcitons in responses to infections (by Salmonella, for example) (Nicholas, 2004).

--Of just under 20,000 genes in C. elegans, about 500 kinases, 185 phosphatases, and 128 phosphoprotein-binding domains are known.  Protein kinases represent the second most abundant protein domain in the worm genome (after seven transmembrane chemoreceptors and ahead of zinc finger transcription factors).  There are a number of kinase signaling cascades which exist in both worms and humans such as the AGC group of kinases (homologous to AKT and PDK1 in mammals), CAMK group (including death associated protein kinases, MAPK-associated kinases, myosin light chain kinase, and phosphorylase kinase), CMGC group (including the cyclin depenednet kinases, GSK-3, MAPKs, and CLK), STE group (including homologs of mammalian RAF, MLK, and TAK1 genes), receptor tyrosine kinases (the largest group of kinsaes in all higher eukaryotes from worms to humans), and the protein-tyrosine kinase group.  The CAMK group of kinases is absent from yeast and help multicellular organisms reach greater complexity.  The RCK family (seven genes in humans) is also absent in yeast.  Worms and humans both have more than twice the number of MAP kinases known in yeast (Plowman, 1999).  Worms, flies, and humans use this pathway in development (Su, 1998). The incorporation of MAP kinase cascades in innate immunity is an ancient animal mechanism, known from nematodes and higher animals (Kim, 2002).

--Nematodes posses two Bcl-2 family members, one of which is pro-apoptotic, the other which is anti-apoptotic.  The two Bcl-2 family members known from flies are both pro-apoptotic as are their mammalian homologs Bok/Mtd (Igaki, 2004).  Expression of the pro-apoptotic nematode protein CED-4 in the cells of flies causes apoptosis, indicating that the cellular mechanisms of apoptosis have been preserved (Kanuka, 1999).  Human Bcl-2 can prevent cell death in nematode cells, indicating that apoptotic pathways have been conserved in animals (Vaux, 1993).

--Nematodes possess a p53 homolog which is expressed throughout the body and regulates cellular responses to stress and damage (Sutcliffe, 2004).

--A tankyrase homolog in nematodes induces apoptosis in response to DNA damage (Gravel, 2004).

 

COELOMATES

--A number of kinase subfamilies are only known in coelomates (but not in C. elegans) such as Jak A, JakB, Syk, Tek, Slob, Ste20 NinaC, CCK4, Musk, Ret, PDGF/VEGFR, Sev, Lisk, Mos, TOPK, Trb, and CDK10 (Manning, 2002).  A number of these are expressed in the nervous system which is more complex in coelomates.  Four of these subfamilies help to regulate the cell cycle (Manning, 2002).  Several kinase families which function in immunology, the nervous system, development, and the control of cell division are shared between flies and humans (Manning, 2002).

--Flies possess p53 homologs which can bind to human p53 targets and overexpression of p53 causes apoptosis in flies (Sutcliffe, 2004). 

The Drosophila protein Eiger is a member of the TNF superfamily which can cause apoptosis (Moreno, 2002).  

--Apoptotic mechanisms are conserved in coelomates given that flies possess cytochrome c, HtrA2/Omi, AIF, and EndoG (Igaki, 2004).  

--C. elegans possesses one caspase while multiple caspases are known in Drosophila.  The activation of caspases by CED-4 is a conserved mechanism (Kankura, 1999). 

--Both mammalian and fly genomes possess a family of enhancer factors with homologs of AP-1, Fos and Jun (Perkins, 1988).

--Mnt and Mlx members of the Myc bHLH protein family control cell division and apoptosis.  Homologs are known in Drosophila (Peyrefitte, 2001).

--Flies have fos and jun (Perkins, 1988)

 

DEUTEROSTOMES

--The duplication of the cytoplasmic gene to form vertebrate muscle and nervous tissue genes occurred after the separation of protostome lineages (Pineda, 2001). 

 

CHORDATES

--Tunicates possess 11 caspases (compared to 14 in mammals and 1 in nematodes) and homologs of both the intrinsic and extrinsic pathways of caspase activation (including the Ced-4, Apaf-1 [intrinsic] and TNF receptors [extrinsic] which are absent in worms) (Dehal, 2002).

 

VERTEBRATES

--The various subfamilies were expanded early in the evolution of vertebrates (Gu, 2003).