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ABC TRANSPORTER SUPERFAMILY AND HELICASE SUPERFAMILY
   ABC transporters and helicases are superfamilies of proteins which are found in all groups of organisms, including bacteria, plants, and vertebrates.   Homologous regions suggest that both are modified versions of the same ancestral genes (Gadsby, 2006).
bacteria flower
snake

  Both of these two superfamilies have similarities in their nucleotide binding domains and some helicases are ATP-dependent, as are the ABC transporters.  They seem to have arisen from one class of ancestral proteins.  Some ABC transporters do not perform any transport and are involved in DNA repair (such as MutS, Rad50, and bacterial UvrA).  These non-transporting ABC family members might be “missing links” between ABC transporters and helicases.  ABC transporters are also homologous to the protein RecA which mediates recombination.   From ancestral transporter/helicases which were present in the early cells, gene duplications and subsequent modifications have produced a diversity of proteins with a wide array of functions.  The many human genes in these families include the genes whose mutations cause cystic fibrosis, the multidrug transporters which must be considered in cancer treatment, and the TAP proteins which are required for the recognition of “self” by the immune cells.    

 

ABC TRANSPORTERS

     The family of ABC-ATPases represent transmembrane proteins which utilize ATP to transport a wide diversity of molecules, ranging from ions to proteins, across the cell membrane.  They are found in all organisms and represent one of the largest families of proteins, which can be broken into a number of subfamilies.  These proteins can be used to both import extracellular molecules and export intracellular molecules (Holland, 1999; Peelman, 2003).   While most function in transport, some are channels, some regulate other channels, and some have functions which do not involve transport.  Many transport specific substrates only while others can transport a number of dissimilar substrates.  (Theodoulou, 2000).  Some ABC transporters seem to be able to regulate other types of membrane channels (Holland, 1999).  More than 2000 ABC transporters had been identified in living organisms and an even greater number (about 6000) proteins which interact with them are known (Dassa, 2001). 

     Most ABC transporters are composed of 5 separate protein domains: 2 ATP binding regions (or nucleotide-binding regions, NBDs), 2 transmembrane regions, and a receptor.  In prokaryotes, most of these domains are encoded by their own separate genes, although genes for these separate domains can be located near each other in operons.  Other transporters are encoded by genes which code for two or more of these domains, resulting from a fusion of these individual genes.  As a result, some ABC transporters are encoded by 4 genes, 3 genes, 2 genes, or 1 single gene.  In humans, “full” ABC proteins possess 2 transmembrane and 2 ATP-binding regions encoded by one single gene and are usually located on the cell membrane.  “Half” ABC proteins possess only one of each of these domains and thus two “half” proteins are required to form a functional channel.  These “half” proteins are typically expressed in the membranes of organelles.    In Drosophila, the three half ABC transporters encoded by the white, brown, and scarlet proteins can form 2 channels for the transport of eye pigments: scarlet-white and brown-white (OMIM, Hung, 1998). While most transporters consist of 6 membrane-spanning regions in the transmembrane domain, the membrane can be crossed from 3 to 11 times (Holland, 1999).

     In the human ABCR transporter, NBD2 (one of the two nucleotide binding regions) was shown to be specific for ATP while NBD1 can bind to any ribonucleotide (ATP, GTP, CTP, and UTP) (OMIM; Holland, 1999).

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Below is the white mutant in Drosophila.

white scarlet
In the image below, a wild type fly (upper fly) is compared to the mutants scarlet and brown.
The image to the right represents three ABC transporters: the HisQMP2 transporter of E.coli made of 4 subunits encoded by 3 genes; the Drosophila eye pigment transporter formed by the products of 2 genes (each encoding half a transporter), and the chloride ion transporter responsible for cystic fibrosis (one gene)
abc
bacteria bacteria

     In bacteria (such as those pictured above), ABC transporters can be used in osmoregulation, transport of bicarbonate, nitrite, nitrate, maltose, trehalose, sugars, ions, peptides, cellobiose, fructose, sulfur, glucose, molybdate, anions, arsenite, heme, manganese, phosphate, and carnitine.  ABC transporters compose 1-2% of the genes in some bacterial genomes such as E. coli (where they are the largest gene family in the genome), Bacillus subtilis, and archaea. (Horlacher, 1998; Liu, 1998; van der Heide, 1999). 

     The trehalose/maltose transport system of the archebacteria Thermococcus and the maltose/maltodextrin transport system of E. coli use homologous ABC transporters coded by malEFG in E. coli.  The binding region of the protein is coded by malE, the membrane portions are coded by malF and malG, and the ATP binding region is coded by malK.  In the cyanobacterium Synechocchus, the operon composing proteins of the cmpABCD complex transport bicarbonate and the similar proteins of the nrtABCD complex transport nitrite and nitrate.  The histidine permease of S. typhimurum and E. coli Is encoded by the HisQMP2 complex: 2 genes encode the transmembrane region (HisQ and HisM) and 2 copies of HisP catalyze ATP hydrolysis. (Horlacher, 1998; Liu, 1998; van der Heide, 1999; Omata, 1999).  Prokaryotic import transporters require an additional protein which binds the substrate in order to function (Dassa, 2001). There seem to be two subfamilies of ABC transporters with the bacterial import transporter subfamily forming a separate group from bacterial export transporters and eukaryotic transporters (Holland, 1999).  A sugar ABC transporter appears to have been spread from archaea Thermococcus litoralis to Pyrococcus furiosus through lateral transfer (Imamura, 2004).  Archaea are depicted below.

archebacteria

     There are more than 100 ABC transporters known in eukaryotes but their substrates are often unknown.  In plants, ABC transporters can transport herbicides (Theodoulou, 2000).  Plants possess homologs of ABC transporters which perform important functions in humans such as MDR and MRP (which are responsible for multiple drug resistance (Theodoulou, 2000).  Some plant transporters affect their interaction with microbes and some are expressed on organelle membranes (Theodoulou, 2000).  At least 29 are known in yeast and almost all human ABC transporters have homologs in yeast (Decottignies, 1997).   ABC transporters responsible for multidrug resistance in yeast (Wolfger, 2001) in addition to the transport of pheromones and organic acids (Holland, 1999).  

     Because of the diversity of functions performed by different ABC transporters, ranging from eliminating harmful compounds to immune signaling to development, mutations in these genes can have a diverse effects in humans.  Mutations in MOAT cause congenital hyperbiliruginemia, those in CFTR cause cystic fibrosis, those in SUR1 cause hyperinsulinemia hypoglycemia,  those in MDR3 cause progressive familial intrahepatic cholestasis, those in SPGP cause abnormal bile secretion and progressive familial cholestasis, and mutations in ALDP cause adrenoleukodystrophy and affects peroxisomes  (Holland, 1999)..

 

 

 

CFTR

     Most mutations in the CFTR gene (the cystic fibrosis transductance regulator) cause cystic fibrosis (CF); others cause the congenital aplasia of the vas deferens in males (CBAVD; with or without CF), nasal polyps (with CF), and the increase of chloride secreted in sweat (without CF).  Although the protein is itself a chloride channel, it also seems to affect other transport proteins such as the outwardly rectifying chloride channels (ORCCs), the chloride-coupled bicarbonate transporter, sodium transport, and can also affect transport at gap junctions.  With the loss of the control of ion movement, the movement of water is affected and the loss of control of bicarbonate movement affects pH.  In patients with CF, body secretions (from the pancreas, respiratory passageways, reproductive tracts, etc.) are more viscous and are more acidic than those of normal individuals.  This viscosity and altered pH also contribute to bacterial infections (OMIM; Theodoulou, 2000).

     The nucleotide binding domains of the CFTR gene (NBD1 and NBD2) are homologous to HisP of E.coli.  Many mutations causing cystic fibrosis occur in these regions; the most common mutations affects the interaction between these domains.  Seventy percent of CF patients have a 3 base pair deletion which removes the amino acid phenylalanine at position 508.  One in 16 caucasians is a carrier for a CFTR mutation (OMIM).  CFTR is not the only chloride channel in cells (nor the most efficient) and there is evidence that CFTR can pump additional molecules such as anti-oxidants, organic anions, and glucouronate (Holland, 1999).

 

    The human gene RNaseP encodes at least 8 separate proteins (some of which process precursor tRNAs) and an essential RNA.  One of the proteins encoded is an ATPase homologous to HisP of ABC transporters (and can be inhibited in a similar fashion) (Li, 2001).

 

     The TAP transporter is composed of a heterodimer consisting of TAP1 and TAP2 transporters, both encoded in the MHC II region.  TAP transports peptides produced by the proteasome to MHC I proteins.  TAP-like proteins are known in humans (where they are most highly expressed in the testes), in plants and in invertebrates (such as nematodes) (Dassa, 2001; Kelly 1992b). 

 

TAP1

     This gene is located within the MHC complex on chromosome 6p21.  It transports peptides from the cytosol to MHCI molecules in the ER and thus is essential for the presentation of peptides to immune cells which allow the recognition of self.

 

TAP2

 

ARSA

--This is one of two human genes homologous to the arsenite transporter in E. coli.

 

ABC SUBFAMILY A

There are twelve known human paralogs of the ABCA subfamily.  Proteins of the ABCA subfamily are known throughout the groups of eukaryotes and are homologous to the ABC subfamily 7 in prokaryotes (Peelman, 2003).

 

ABCA1

--This transporter (also known CERP, the cholesterol efflux regulator protein) is involved in cholesterol transport and is located in the cell membrane and on the Golgi.  Normal cells pump out about 0.1% of the intracellular cholesterol per minute.  If it is blocked, lipids don’t leave cells.  Mutations result in HDL deficiencies and Tangier disease.

 

ABCA2

--This is a duplicate copy of ABCA1 also located on chromosome 9q.

 

ABCA3

--This transporter has 2 repeated regions, each with 6 transmembrane domains and 1 ATP binding domain.  Its homolog in C. elegans (ced-7) is a protein which functions in adhesion in dying cells and the cells engulfing them.  This suggests that the mechanism of engulfing cells after apoptosis is conserved from nematodes through mammals.

 

ABCA4

--This transporter is retina specific and is expressed in photoreceptor cells.  Mutations cause Stargadt disease, macular degeneration, retinitis, cone-rod dystrophy, fundus flavimaculatus, and the accumulation of lipofuscin fluorophore.  The cells of a chick retina are visible in the following image.

retina

ABCA5

ABCA5 is expressed in skeletal muscle.

 

ABCA6

ABCA6 is expressed in the liver.

liver

ABCA7

--This transporter is expressed throughout the body, with its highest expression in the fetal liver.

 

ABCA8

ABCA8 is expressed in the ovary.

 

ABCA9

ABCA9 is expressed in the heart.

 

ABCA10

ABCA10 is expressed in skeletal muscle.

 

ABC11

 

ABC12

 

 

ABC SUBFAMILY B

ABCB1

     This transporter (also known as P glycoprotein 1) is involved in multidrug resistance, pumping drugs out of the cell membrane.  Its expression is increased in all mammalian cells which are multidrug resistant and decreases the effectiveness of anti-HIV protease inhibitors.  It also pumps chloride ions (and is structurally similar to the CFTR gene whose protein does the same).  Mutant mice are normal but have an increased sensitivity to drugs.  Variations in the activity of this transporter in pregnant women might vary the concentration of drugs that fetuses are exposed to (OMIM). The P-gp (MDR1) family subfamily of ABC transporters seems to be specific to eukaryotes and include MDR1-like proteins which are responsible for multiple drug resistance and other subfamily members which pump bile salts and phosphatidyl choline (Dassa, 2001).

     Cancer cells which develop resistance to one type of chemical can simultaneously develop resistance to unrelated molecules (mutidrug resistance). This often occurs because of overexpression of MDR1. Other ABC transporters outside the MDR1 group (such as MRP) can also transport drugs used in cancer therapy (Theodoulou, 2000). In humans, MRD1 can transport a variety of drugs, analgesics, β amyloid peptide, lipids, detergents, hormones, cholesterol, and antihistamine (Holland, 1999)..

 

ABCB6

     This transporter has its highest expression in the heart and skeletal muscle (pictured below) and may transport iron and sulfur from the mitochondria.  Mutations can cause fetal death associated with abnormal mitochondrial iron metabolism.

 

cardiac

ABCB7

     This transporter is expressed in a variety of tissues (but not the brain) and the protein is located on the inner mitochondrial membrane where it may transport heme from the mitochondria to the cytosol.  Mutations cause sideroblastic anemia.

 

ABCB8 is also used in the mitochondria.

 

ABCB9 has 10 transmembrane domains and functions in lysosmal membranes.

 

ABCB10 has its highest expression in the bone marrow.  There is a pseudogene located on chromosome 15.

 

ABCB11 is a bile salt export pump (BSEP).  ABC transporters pump the majority of bile including bile acids, phospholipids, and organic acids.  Mutations cause progressive intrahepatic cholestasis (human liver cells pictured below).

liver

ABC SUBFAMILY C

ABCC1

--This transporter transports a lekotriene which is involved in the migration of dendritic cells to lymph nodes.

 

ABCC2

     This transporter pumps anions from hepatocytes into bile and is also involved in multidrug resistance.  Mutations cause the Dubin-Johnson syndrome in which there is a higher level of bilirubin in the blood and an increased excretion of certain substances in urine (liver cells pictured below).

liver

ABCC3  is involved in both bile production and multidrug resistance.

 

 ABCC4 is involved in multidrug resistance and has 12 transmembrane regions.

 

ABCC5 is involved in multidrug resistance.

 

In humans, the ABCC13 protein contains only 6 exons of the 28 which are present in the gene due to a frameshift mutation which prevents the other exons from being translated.  The complete protein is expressed in Old World monkeys while a shared 11 base pair deletion (which results in the frameshift) exists in humans, chimps, and gorillas.  Although the gene is expressed in the colon, bone marrow, salivary gland, and fetal liver the truncated transcript cannot function as a transporter.  The gene is thought to be in the process of becoming a pseudogene (Annilo, 2004).

 

ABC SUBFAMILY D

      Three members of this subfamily, ABCD2, ABCD3, and ABCD4 are transporters found in peroxisomal membranes.  They are all “half transporters” which must form dimers with other half transporters.  Yeast homologs are also located in peroxisomes where they function in the beta oxidation of fatty acids (OMIM; Dassa, 2001). 

 

ABCD2 mutations impairs the beta oxidation of long-chain fatty acids and results in adrenoleukodystrophy.

 

ABCD3 is located in almost all eukaryotic cells.  Mutations cause Zellweger syndrome.

 

ABCF1 has no transmembrane domain.  It is expressed in all human tissues and TNFa increases its expression.

 

ABCG1

     This transporter is the homolog of white, scarlet, and brown in Drosophila.  In Drosophila, these half transporters function in the transport of eye pigment precursors.  In humans, macrophages (pictured below)use this transporter for cholesterol uptake.

monocyte

ABCG2

     This transporter is highly expressed in the placenta and has been involved in multidrug resistance cases of breast cancer.

 

ABCG5 and ABCG8

     These two genes exist in tandem on 2p21, resulting from duplications of an ancestral gene.  They are half transporters that can form heterodimers. They are highly expressed in the liver and expression increases with increase lipid in the diet.  They limit the absorption of lipid and promote its excretion into bile.  Mutations in these genes cause sitosterolemia in which too much lipid is absorbed, too little is excreted, and atherosclerosis results.

 

ABC transporters exist in mitochondrial membranes, which is not surprising given the use of ABC transporters in prokaryotes and the evidence of an endosymbiotic origin for mitochondria (Lill, 2001).  Two mitochondrial transporters in humans are homologous to the Atm1p transporters in yeast mitochondria and are involved in iron usage.  Two additional human mitochondrial proteins are homologous to the yeast mitochondrial proteins Mdl 1p and Mdl 2p.  All of these genes are members of the MDR subfamily of ABC transporters (Lill, 2001).

 

MTABC3 mutations may cause lethal neonatal syndrome (Lill, 2001).

 

Mdl 1p

 

Mdl 2p. 

 

ATM is involved in the maintenance of mitochondrial DNA and another is involved in interactions between ribosomes and tRNA  (Decottignies, 1997).

 

ABC7 mutations cause X-linked sideroblastic anemia and cerebellar ataxia (Lill, 2001).

 

MRP1 possesses an extra membrane spanning domain (Holland, 1999).

 

HELICASE SUPERFAMILY

      Helicases typically use ATP to unwind DNA or RNA (thus using ATP and binding to nucleotides are characteristics which they share with ABC proteins). 

The ATP binding regions of both ABC cassette transporters and helicases share homologous regions such as the Walker A- and B- motifs.  The ABC family members which interact with DNA and which are not known to function in transport may represent relics which date back to shortly after these two families diverged (Geourjon, 2001)

     Helicases which bind DNA can function in DNA replication, DNA repair, and even control of gene expression.  Those which bind RNA can function in transcription, translation, RNA processing, and transport of mRNA from the nucleus.  There are a variety of helicases in the human genome, many of which are members of subfamilies which have ancient origins and are widely distributed among organisms (OMIM).

 

a) ReqQ-like family

     Req-like proteins are human homologs of the helicase in E. coli which unwinds DNA.

--ReqQ-like 2 mutations are the cause of Werner syndrome which causes premature aging; children can show many symptoms of old age and can die before they reach their teens

--ReqQ-like 3 mutations cause genetic instability caused by hypermutability and high levels of recombination.  The normal protein seems to encode an anti-recombinase that suppresses tumor formation.

--ReqQ-like 4 mutations cause the premature aging of Rothmind-Thomson syndrome.

 

b) DEAD/H Box RNA helicases

     The DEAD/H Box family of helicases is known throughout the eukaryotes (Roussell, 1993).  This family has a number of conserved regions, including a Asp-Glu-Ala-Asp (DEAD) region. 

--DDX6 is also known as Oncogene Rck and is overexpressed in some tumors

            --DDX9 can unwind double-stranded DNA and RNA

            --DDX15 is a pre-mRNA splicing factor

            --DDX19 is located in nuclear pores and functions in mRNA transport

--BRCA-interacting protein interacts with BRCA1; mutations in this gene cause early onset breast cancer

 

c) DBX and DBY are located on the sex chromosomes; DBX is not inactivated in the formation of Barr bodies

 

d) Nucleolar Protein H is a helicase expressed in the fetal and adult brain.

 

e) Eukaryotic Translation Initiation Factors EIF4A and EIF4B

--These proteins bind to the mRNA cap and unwind the secondary structure of mRNA to begin transcription.  EIF4A is overexpressed in some tumors.

 

f) C10ORF2

     This gene encodes the protein twinkle which is a helicase active in the mitochondrial nucleoid regions.  Mutations cause ophthalmoplegia.

 

g) ATRX

     ATRX is a member of the helicase superfamily and mutations in humans can cause thalassemia, mental retardation, and sex reversal.  It seems to be involved in gene regulation, perhaps at the chromatin level.  ATRY in marsupials is active and expressed in the testes.  ATRX is involved in gonadal development downstream of SRY, SOX9, and AMH.  ATRX is not expressed in the marsupial testis, which is the predominant expression site of ATRY.  Marsupials have ATR helicases on both their X and Y chromosomes and it is possible that this gene was involved in gender determiation before the evolution of SRY (OMIM; Pask, 2000).

 

h) CHD family

--CHD1 binds DNA and may be involved in chromosome structure and transcription.

--CHD3 mutations cause dematomyositis.

--CHD4 is involved in nucleosome remodeling.

 

i)HELLS is a lymphoid specific helicase required for T cell proliferation.

 

j) HELZ is a helicase with a zinc finger domain involved in embryonic development.

 

k) RuvBL genes (1 and 2)

    These helicases are homologous to bacterial helicases involved in recombination and double stranded break repair.

 

RecA FAMILY

     In E. coli, RecA is a protein which mediates recombination.  In yeast, the homologous protein is important both in DNA replication and the recombination which occurs in meiosis.

 

RAD51—this protein forms a complex with both BRCA1 and BRCA2 proteins.  Some mutations cause breast cancer while other increase the risk of breast cancer but only in those women who are carriers for BRCA mutations.

 

RAD51-like 1 is expressed in areas where recombination occurs, such as the ovary, testis, thymus and spleen.

 

RAD51-like 3 is most highly expressed in the testis (pictured below).

Dmc1 is involved in the synapsis of homologous chromsomes in meiosis.  Mutations cause sterility in which meiosis stops in prophase I.

One RNA helicase in nematodes possesses zinc fingers of retroviral origin (Roussell, 1993).