Dissertation (PhD)--University of Stellenbosch, 2003. / ENGLISH ABSTRACT: In the yeast Saccharomyces cerevtstee, two biochemical pathways ensure that
activated cytoplasmic or peroxisomal acetyl-groups are made available for
mitochondrial energy production when the cells utilise non-fermentable carbon
sources. The first pathway is the glyoxylate cycle, where two activated acetyl-groups
are incorporated into each cycle, which releases a C4 intermediate. This intermediate
is then transported to the mitochondria where it can enter the tricarboxylic acid cycle.
The second pathway is the carnitine shuttle. Activated acetyl-groups react with
carnitine to form acetylcarnitine, which is then transported to the mitochondria where
the acetyl group is transferred.
In this study it was shown that the deletion of the glyoxylate cycle specific citrate
synthase, encoded by CIT2, results in a strain that is dependent on carnitine for
growth on non-fermentable carbon sources. Using a /::"cit2 strain, mutants affected in
carnitine-dependent metabolic activities were generated. Complementation of the
mutants with a genomic library resulted in the identification of four genes involved in
the carnitine shuttle. These include: (i) the mitochondrial and peroxisomal carnitine
acetyltransferase, encoded by CAT2; (ii) the outer-mitochondrial carnitine
acetyltransferase, encoded by YA T1; (iii) the mitochondrial carnitine translocase,
encoded by CRC1; and (iv) a newly identified carnitine acetyltransferase, encoded by
YAT2. All three carnitine acetyltransferases are essential in a carnitine-dependent
strain.
The dependence on exogenous carnitine of the /::"cit2 strain when grown on nonfermentable
carbon sources suggested that S. cerevisiae does not biosynthesise
carnitine. Measurements using electrospray mass spectrometry confirmed this
hypothesis. As a result an investigation was initiated into carnitine biosynthesis in
order to genetically engineer a S. cerevisiae strain that could endogenously
biosynthesise carnitine.
The filamentous fungus, Neurospora crassa, was one of the first organisms used
in the seventies to identify the precursor and intermediates of carnitine biosynthesis.
However, it was only about twenty years later that the first genes encoding these
enzymes where characterised. Carnitine biosynthesis is a four-step process, which
starts with trimethyllysine as precursor. Trimethyllysine is converted to hydroxytrimethyllysine
by the enzyme trimethyllysine hydroxylase (TMLH). Hydroxytrimethyllysine
is cleaved to trimethylamino-butyraldehyde by the
hydroxytrimethyllysine aldolase (HTMLA) releasing glycine. Trimethylaminobutyraldehyde
is dehydrogenated to trimethylamino-butyrate (y-butyrobetaine) by
trimethylamino-butyraldehyde dehydrogenase (TMABA-DH). In the last step, ybutyrobetaine
is converted to t-carnltine by y-butyrobetaine hydroxylase (BBH).
The N. crassa TMLH homologue was identified in the genome database based
on the protein sequence homology of the human TMLH. Due to the high amount of introns predicted for this gene, the cDNA was cloned and subjected to sequencing,
which then revealed that the gene indeed had seven introns. Functional expression
of the gene in S. cerevisiae and subsequent enzymatic analysis revealed that the
gene coded for a TMLH. It was therefore named cbs-1 for "carnitine biosynthesis
gene no. 1JJ. Most of the kinetic parameters were similar to that of the human TMLH
enzyme. Following this, a genomic copy of the N. crassa BBH homologue was cloned
and functionally expressed in S. cerevisiae. Biochemical analysis revealed that the
BBH enzyme could biosynthesise L-carnitine from y-butyrobetaine and the gene was
named cbs-2. In addition, the gene could rescue the growth defect of the carnitinedependent
Scii? strain on non-fermentable carbon sources when y-butyrobetaine was
present. This is the first report of an endogenously carnitine biosynthesising strain of
S. cerevisiae.
The cloning of the remaining two biosynthesis genes presents particular
challenges. To date, the HTMLA has not been characterised on the molecular level
making the homology-based identification of this protein in N. crassa impossible.
Although the TMABA-DH has been characterised molecularly, the protein sequence
is conserved for its function as a dehydrogenase and not conserved for its function in
carnitine biosynthesis, as in the case of TMLH and BBH. The reason for this is
probably due to the fact that the enzyme is involved in other metabolic processes.
The use of N. crassa carnitine biosynthesis mutants would probably be one way in
which to overcome these obstacles.
The !1cit2 mutant proved useful in studying carnitine related metabolism. We
therefore searched for suppressors of !1cit2, which resulted in the cloning of RAS2. In
S. cerevisiae, two genes encode Ras proteins, RAS1 and RAS2. GTP-bound Ras
proteins activate adenylate cyclase, Cyr1 p, which results in elevated cAMP levels.
The cAMP molecules bind to the regulatory subunit of the cAMP-dependent kinase
(PKA), Bcy1 p, thereby releasing the catalytic subunits Tpk1 p, Tpk2p and Tpk3p. The
catalytic subunits phosphorylate a variety of regulators and enzymes involved in
metabolism. Overexpression of RAS2 could suppress the growth defect of the Sclt?
mutant on glycerol. In general, overexpression of RAS2 enhanced the proliferation of
wild-type cells grown on glycerol. However, the enhancement of proliferation was
much better for the !1cit2 strain grown on glycerol. In this respect, the retrograde
response may play a role. Overexpression of RAS2 resulted in elevated levels of
intracellular citrate and citrate synthase activity. It therefore appears that the
suppression of !1cit2 by RAS2 overexpression is a result of the general upregulation
of the respiratory capacity and possible leakage of citrate and/or citrate synthase
from the mitochondria. The phenotype of RAS2 overexpression contrasts with the
hyperactive RAS2val19 allele, which causes a growth defect on glycerol. However,
both RAS2 overexpression and RAS2val19activate the cAMP/PKA pathway, but the
RAS2val19dependent activation is more severe. Finally, this study implicated the
Ras/cAMP/PKA pathway in the proliferation effect on glycerol by showing that in a
Mpk1 strain, the growth effect is blocked. However, the enhanced proliferation was still observed in the Mpk2 and Mpk3 strains when RAS2 was overexpressed.
Therefore, it seems that Tpk1 p plays an important role in growth on non-fermentable
carbon sources, a notion that is supported by the literature. / AFRIKAANSE OPSOMMING: In die gis Saccharomyces cerevtstee, is daar twee metaboliese weë waarmee
geaktiveerde asetielgroepe na die mitochondrium vervoer kan word wanneer die sel
op nie-fermenteerbare koolstofbronne groei. Die een weg is die glioksilaatsiklus,
waar die geaktiveerde asetielgroepe geïnkorporeer word in die siklus en dan
vrygestel word as Ca-intermediêre. Hierdie intermediêre word dan na die
mitochondrium vervoer waar dit in die trikarboksielsuursiklus geïnkorporeer word. Die
ander weg is die karnitiensiklus, waar geaktiveerde asetielgroepe met karnitien
reageer om asetielkarnitien te vorm wat dan na die mitochondrium vervoer word waar
dit die asetielgroep weer vrygestel.
Hierdie studie het getoon dat die delesie van die glioksilaatsiklus spesifieke
sitraatsintetase, gekodeer deur CIT2, die gisras afhanklik maak van karnitien vir groei
op nie-fermenteerbare koolstofbronne. Deur gebruik te maak van 'n ócit2 gisras, kon
mutante, wat geaffekteer is in karnitien-verwante metaboliese aktiwiteite, gegenereer
word. Komplementering van die mutante met 'n genomiese biblioteek het gelei tot die
identifisering van vier gene betrokke by die karnitiensiklus. Hierdie gene sluit in: (i)
die mitochondriale en die peroksisomale karnitienasetieltransferase, gekodeer deur
CAT2; (ii) die buite-mitochondriale karnitienasetieltransferase, gekodeer deur YAT1;
(iii) die mitochondriale karnitientranslokase, gekodeer deur CRC1; en (iv) 'n nuutgeïdentifiseerde
karnitienasetieltransferase, gekodeer deur YAT2. Daar benewens, is
ook gewys dat al drie karnitienasetieltransferases noodsaaklik is in 'n karriltienafhanklike
gisras.
Die afhanklikheid van eksogene karnitien van die ócit2 gisras, wanneer dit
gegroei word op nie-fermenteerbare koolstofbronne, was aanduidend dat
S. cerevisiae nie karnitien kan biosintetiseer nie. Metings deur middel van
elektronsproeimassaspektrometrie het hierdie veronderstelling bevestig. Gevolglik is
'n ondersoek deur ons geïnisieer in die veld van karnitienbiosintese om 'n
S. cerevisiae gisras geneties te manipuleer om karnitien sodoende endogenies te
biosintetiseer.
Die filamentagtige fungus, Neurospora crassa, was een van die eerste
organismes wat in die sewentiger jare gebruik is om die voorloper en intermediêre
van karnitienbiosintese te identifiseer. Dit was egter eers sowat twintig jaar later dat
die eerste gene wat vir hierdie ensieme kodeer, gekarakteriseer is.
Karnitienbiosintese is 'n vierstap-proses wat met trirnetlellisten as voorloper begin.
Trimetiellisien word omgeskakel na hidroksi-trimetiellisien deur die ensiem
trimetiellisienhidroksilase (TMLH). Hidroksietrimetlelllsien word dan gesplits om
trimetielaminobuteraldehied te vorm deur die werking van die
hidroksitrimetiellisienaldolase (HTMLA) met die gevolglike vrystelling van glisien.
Trimetielaminobuteraldehied word dan na trimetielaminobuteraat (y-butirobeteïen)
deur trimetielaminobuteraldehied dehidrogenase (TMABA-DH) gedehidrogeneer. In die laaste stap word y-butirobeteïen deur middel van die y-butirobeteïen hidroksilase
(BBH) na L-karnitien omgeskakel.
Op grond van die proteïenvolgordehomologie in die genoomdatabasis tussen die
menslike TMLH en N. crassa se TMLH is laasgenoemde geïdentifiseer. As gevolg
van die groot getal introns wat vir hierdie geen voorspel is, is die cDNA-weergawe
daarvan gekloneer en aan volgordebepaling onderwerp. Dit het getoon dat die geen
inderdaad sewe introns bevat. Funksionele uitdrukking van die geen in S. cerevisiae
en ensiematiese analise het getoon dat die geen vir 'n TMLH kodeer en is gevolglik
cbs-1 genoem; dit staan vir "karnitien biosintese geen no. 1tt. Meeste van die
kinetiese parameters was ook soortgelyk aan die van die menslike TMLH-ensiem.
Hierna is 'n genomiese kopie van N. crassa se BBH-homoloog gekloneer en
funksioneel in S. cerevisiae uitgedruk. Biochemiese analise het getoon dat die
uitgedrukte BBH-ensiem L-karnitien vanaf y-butirobeteïen kan biosintetiseer en die
geen is cbs-2 genoem. Daar benewens kon die geen die groeidefek van die
karnitien-afhanklike tlcit2-gisras ophef wanneer dit op nie-fermenteerbare
koolstofbronne in die teenwoordigheid van y-butirobeteïen aangekweek is. Hierdie is
die eerste verslag oor 'n endogeniese karnitien-biosintetiserende ras van
S. cerevisiae.
Die klonering van die oorblywende twee karnitienbiosintetiserende gene het
sekere uitdagings. Tot op datum, is die HTMLA nog nie tot op genetiese vlak
gekarakteriseer nie, wat dan die homologie-gebaseerde identifikasie van hierdie
proteïen in N. crassa onmoontlik maak. Alhoewel die TMABA-DH geneties
gekarakteriseer is, is die proteïenvolgorde ten opsigte van sy funksie as 'n
dehidrogenase gekonserveer, maar nie vir sy funksie in karnitienbiosintese soos in
die geval van TMLH en BBH nie. Die rede hiervoor is moontlik omdat die ensiem ook
in ander metaboliese prosesse betrokke is. Die gebruik van N. crassa
karnitienmutante sal moontlik een manier wees om hierdie probleme te oorkom.
Die tlcit2-mutant het handig te pas gekom vir die bestudering van karnitienverwante
metabolisme. Dus is daar vir onderdrukkers van die tlcit2-mutant gesoek
wat gelei het tot die klonering van die RAS2-geen. In S. cere visiae , kodeer twee
gene vir Ras-proteïene, RAS1 en RAS2. GTP-gebonde Ras-proteïene aktiveer
adenilaatsiklase, Cyr1 p, wat verhoogde intrasellulêre cAMP-vlakke tot gevolg het.
Die cAMP bind aan die regulatoriese subeenheid van die cAMP-proteïenkinase
(PKA), Bcy1 p, en daardeur word die katalitiese subeenhede, Tpk1 p, Tpk2p en
Tpk3p, vrygestel. Die katalitiese subeenheid fosforileer 'n verskeidenheid van
reguleerders en ensieme betrokke by metabolisme. Ooruitdrukking van RAS2 het die
groeidefek van die tlcit2-mutant op gliserolonderdruk. Oor die algemeen, verbeter
die ooruitdrukking van RAS2 die proliferasie van die wildetipe op gliserol bevattende
media. Alhoewel, die verbetering van proliferasie was baie meer opmerklik in die
tlcit2-gisras. In hierdie verband, speel die gedegenereerde response dalk 'n rol.
Ooruitdrukking van RAS2 het verhoogde intrasellulêre vlakke van sitraat- en
sitraatsintetase-aktiwiteit tot gevolg gehad. Dit wou dus voorkom asof die onderdrukking van die ócit2-groeidefek deur RAS2 se ooruitdrukking die gevolg was
van algemene opreguiering van respiratoriese kapasiteit en die lekkasie van sitraat
en/of sitraatsintetase uit die mitochondria. Die fenotipe van RAS2 ooruitdrukking
kontrasteer die hiperaktiewe RAS2va
/
19 alleel, wat 'n groeidefek op gliserol media
veroorsaak. Alhoewel beide RAS2-00ruitdrukking en RAS2va
/
19 die cAMP/PKA-weg
aktiveer, is gevind dat die RAS2va/19-afhanklike aktivering strenger is. Ten slotte, die
cAMP/PKA-weg is in die proliferasie effek op gliserol media geïmpliseer deur te wys
dat in 'n Mpk1-gisras, die groeieffek geblokkeer is. Alhoewel, die verbeterde
proliferasie is steeds waargeneem in die Mpk2-en Mpk3-gisrasse toe die RAS2-geen
ooruitgedruk is. Dus, dit wil voorkom asof Tpk1 p 'n belangrike rol in die groei van
gisselle op nie-fermenteerbare koolstofbronne speel; 'n veronderstelling wat deur die
literatuur ondersteun word.
| Identifer | oai:union.ndltd.org:netd.ac.za/oai:union.ndltd.org:sun/oai:scholar.sun.ac.za:10019.1/49753 |
| Date | 12 1900 |
| Creators | Swiegers, Jan Hendrik |
| Contributors | Bauer, F. F., Pretorius, I. S., Stellenbosch University. Faculty of Science. Dept. of Microbiology. |
| Publisher | Stellenbosch : Stellenbosch University |
| Source Sets | South African National ETD Portal |
| Language | en_ZA |
| Detected Language | English |
| Type | Thesis |
| Format | 144 p. : ill. |
| Rights | Stellenbosch University |
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