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Aspergillus niger genomics: Past, present and into the
future
SCOTT E. BAKER
Fungal Biotechnology Team, Pacific Northwest National Laboratory, Richland, Washington, USA
Aspergillus niger is a filamentous ascomycete fungus that is ubiquitous in the
environment and has been implicated in opportunistic infections of humans. In
addition to its role as an opportunistic human pathogen, A. niger is economically
important as a fermentation organism used for the production of citric acid.
Industrial citric acid production by A. niger represents one of the most efficient,
highest yield bioprocesses in use currently by industry. The genome size of A. niger
is estimated to be between 35 and 38 megabases (Mb) divided among
eight chromosomes/linkage groups that vary in size from 36 Mb. Currently,
there are three independent A. niger genome projects, an indication of the
economic importance of this organism. The rich amount of data resulting from
these multiple A. niger genome sequences will be used for basic and applied
research programs applicable to fermentation process development, morphology
and pathogenicity.
Keywords Aspergillus niger, genome, wildtype, mutant
Introduction
Aspergillus niger is a filamentous ascomycete fungus
that is ubiquitous in the environment and has been
implicated in opportunistic infections of humans [1].
A. niger is most widely known for its role as a citric
acid producer [2]. With production of citric acid at
over one million metric tons annually, A. niger citric
acid production serves as a model fungal fermentation
process. As a common member of the microbial
communities found in soils, A. niger plays a signifi-
cant role in the global carbon cycle. This organism is
a soil saprobe with a wide array of hydrolytic and
oxidative enzymes involved in the breakdown of plant
lignocellulose. A variety of these enzymes from A.
niger are important in the biotechnology industry. A.
niger is also an important model organism for several
important research areas including the study of
eukaryotic protein secretion in general, the effects
of various environmental factors on suppressing or
triggering the export of various biomass degrading
enzymes, molecular mechanisms critical to fermenta-
tion process development, and mechanisms involved
in the control of fungal morphology.
Currently, the genomes of three different strains of
A. niger have been sequenced (Table 1). Two of the
strains sequenced, NRRL 3 (ATCC 9029, CBS 120,
N400) and ATCC 1015 (NRRL 328, CBS 113) are
wildtype strains, while the other strain CBS 513, a
derivative of NRRL 3122 (ATCC 22343, CBS 115989)
was isolated after mutagenesis and selection for im-
proved glucoamylase production [S. Peterson, perso-
nal communication]. Most recently, in 2005, the
genome of A. niger ATCC 1015, a wildtype, historic
strain was used in research that resulted in the first
patented citric acid process [3], that was accepted for
sequencing through the US Department of Energy
(DOE) Microbial Genome Program (MGP). Organ-
isms accepted by this program are sequenced by
the DOE’s Joint Genome Institute (JGI). Another
wildtype A. niger strain, NRRL 3, was sequenced by
Integrated Genomics, a US based company. Finally,
CBS 513, a derivative of a mutant strain, NRRL
3122 was sequenced by a Netherlands based company,
DSM [4,5].
Correspondence: Scott E. Baker, Fungal Biotechnology Team, Pacific
Northwest National Laboratory, 902 Battelle Blvd., MSIN: K2-12,
Richland, Washington 99352, USA. Tel: /1 509 372 4759. Fax: / 1
509 372 4732. E-mail: scott@pnl
– 2006 ISHAM DOI: 10/
Medical Mycology September 2006, 44 , S17 S
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Wildtype strains, ATCC 1015 and NRRL 3
In collaboration with the US Department of Energy
(DOE) Joint Genome Institute (JGI), the Pacific
Northwest National Laboratory Fungal Biotechnology
Team has led a genome sequencing project for A. niger,
strain ATCC 1015. Currently, an /8 shotgun
sequence assembly has been generated by the JGI.
The /8 coverage was generated from three differ-
ent genomic libraries, with inserts of 3 kb, 8 kb and 40
kb. Paired end sequences from the 3 kb and 8 kb
libraries each account for approximately 4X coverage,
while the 40 kb library was sequenced to roughly 0 /
coverage, also with paired ends. The resulting draft
sequence assembled into less than 150 scaffolds. Both
automated annotation and genome finishing (gap
closure) efforts are underway. Manual gene annotation
began in April 2006 after the release of the genome
sequence (jgi.doe/aspergillus with de-
posit into Genbank upon completion of manual
annotation).
In parallel with the genome sequencing project, an A.
niger (ATCC 1015) expressed sequence tag (EST)
project was also launched at the JGI. Two sets of
approximately 15,000 ESTs were sequenced from
cDNA libraries generated from RNA pooled from an
A. niger citric acid production time course (24, 48, 72,
96 and 120 h after spore inoculation) and RNA pooled
from A. niger vegetative growth under a wide variety of
nutritional conditions (corn fiber, rapeseed meal, a mix
of purified lignin, cellulose, hemicellulose and protein,
wheat bran, glucose, lactose, arabinose, starch/maltose,
xylose, carbon limited, nitrogen/carbon limited). Com-
bined with sequences already available in GenBank [6],
the JGI generated ESTs will be used to aid in gene
annotation.
ATCC 1015 is also notable as the parent strain of
ATCC 11414 (NRRL 2270), an A. niger strain used in
citric acid production studies [7,8]. ATCC 11414 was
derived from a subculture of ATCC 1015 that displayed
improved characteristics with regard to citric acid
production [7].
The genome of another A. niger wildtype strain
which produces high quantities of gluconic acid,
NRRL 3 [9,10], was sequenced by Integrated Geno-
mics, a company based in the United States. The
sequence was purchased in 2004 by the Fungal
Biotechnology Team at the Pacific Northwest National
Laboratory under a Laboratory Directed Research and
Development (LDRD) program whose research pro-
gram centered on biobased products from fungal
bioprocesses. Interestingly, the A. niger strain N
(ATCC 64974) which has been used for mitotic
recombination studies and generation of a genetic
map was derived as a ‘short conidiophore’ mutant
from A. niger strain NRRL 3 [11,12]. The approximate
6 / shotgun sequence coverage of A. niger strain
NRRL 3 genome was generated from paired end
sequences from a 12 kb insert genomic library. The
assembly of the sequence was accomplished using the
PHRAP assembly package and resulted in over 9000
contigs (paired end information was not used in the
assembly).
Protein production strain, A. niger strain CBS
513.
A Dutch company, DSM, sequenced the genome of
the A. niger strain, CBS 513 [4,5]. This strain was
Table 1 Comparison of genome projects.
Aspergillus niger genome
sequencing program comparison
Sponsors 0 /Characteristics ¡/
Integrated Genomics DSM DOE OBER Microbial
Genome Program/
Joint Genome Institute (JGI)
Strain Wild-type
(NRRL 3)
Mutant (CBS 513) Wild-type (ATCC 1015)
Project chronology 2000 2000
Public release, pending
2005
Draft sequence public
released, April 2006;
Ongoing sequence gap
fillingfinishing
Aspergillus niger basepairs in
scaffolds
33 Mb 35 Mb 37 Mb
Sequencing method Shotgun BAC tiling Shotgun
Coverage / 6 / /7 / /8 /
Genomic library insert size 1 2 kb BAC 3 kb 8 kb 40 kb
Number of contigs or scaffolds /9000 contigs 19 scaffolds 143 scaffolds
Estimated number of predicted genes /14,000 /14,000 /11,
S18 Baker
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distinct strain lineages will enable identification of
single nucleotide polymorphisms (SNPs). The SNPs
that are identified could be used in population genetic
studies of both A. niger environmental and patient
isolates. Furthermore, SNPs could be useful in improv-
ing the A. niger genetic map for use in mapping the
genetic differences between wildtype and improved
strains. It will be especially interesting to compare
the sequences of the A. niger wildtype strains with
the CBS 513 protein production strain that has
undergone mutagenesis. While it may prove hard
to separate natural variation from the effects of
mutagens, this comparison could generate interesting
data regarding the genes that are important for protein
secretion.
The release of each A. niger genomes sequence
database will accelerate molecular genetic analysis of
genes involved in morphology and cell signaling, two
processes important for A. niger as both a pathogen
and fermentation organism. Molecular genetic tech-
niques for analysis of genes in A. niger are well esta-
blished; the sequenced A. niger genome will allow
researchers the ability to quickly identify and delete,
tag and/or overexpress genes and gene families whose
role in human pathogenicity has been established in
other aspergillosis causative species such as Aspergillus
fumigatus.
The genus Aspergillus is well represented with regard
to completed and in-progress genome sequencing
projects. Recently, analyses of three Aspergillus gen-
omes, A. fumigatus, Emericella nidulans and Aspergillus
oryzae were published [16 18]. Genome projects for
Aspergillus flavus, Aspergillus clavatus, Aspergillus
terreus and Neosartorya fischeri are ongoing. The
plethora of Aspergilli genome sequencing projects is a
strong foundation on which to build comparative
genomics studies. As more genome projects move
from sequencing into data analysis, a high level snap-
shot of each organism’s biology will emerge. Elucida-
tion of the major differences at the genome level
between species whose potential to infect humans
differs greatly has the potential to open up novel
avenues of research that might not have been obvious
previously. Already, we know that the size of Aspergilli
genomes may vary by up to 10 Mb [16 18].
With the release of the JGI generated A. niger
genome sequence database and the pending release
(as of this writing) of the DSM generated A. niger
genome sequence database, the community of research-
ers with interest in this organism are poised to make
important contributions that span across basic biolo-
gical research, evolutionary biology and industrial and
medical mycology. The availability of genome sequence
data and gene model prediction allow proteomic and
transcriptomic analysis at a global level to become
much more straight forward and more accessible. The
important test that lies ahead of these researchers will
be to successfully synthesize and fully utilize the
different types of data proteome, transcriptome,
metabolome that spin out of the A. niger genome
sequence.
Acknowledgements
The author wishes to thank Linda Lasure for helpful
advice and Jon Magnuson, Ken Bruno and Ellen
Panisko for their excellent review of the manuscript.
The author also wishes to thank the scientists at the
DOE Joint Genome Institute where this project is
ongoing. Sequencing of A. niger ATCC 1015 per-
formed under the auspices of the US Department of
Energy’s Office of Science, Biological and Environ-
mental Research Program and the by the University
of California, Lawrence Livermore National Labora-
tory under Contract No. W-7405-Eng-48, Lawrence
Berkeley National Laboratory under contract No.
DE-AC03-76SF00098 and Los Alamos National Lab-
oratory under contract No. W-7405-ENG-36.
References
1 Perfect JR, Cox GM, Lee JY, et al. The impact of culture
isolation of Aspergillus species: a hospital-based survey of
aspergillosis. Clin Infect Dis 2001; 33 : 1824 1833.
2 Magnuson J, Lasure L. Organic acid production by filamentous
fungi. In: Tkacz J, Lange L (eds). Advances in Fungal Biotechnol-
ogy for Industry, Agriculture, and Medicine. New York: Kluwer
Academic & Plenum Publishers, 2004: 307 340.
3 Currie JN. Citric acid fermentation. J Biol Chem 1917; 31 : 15 37.
4 van Dijck PWM, Selten GCM, Hempenius RA. On the safety of a
new genration of DSM Aspergillus niger enzyme production
strains. Reg Tox Pharm 2003; 38 : 27 35.
5 van de Vondervoort PJI, Langeveld SMJ, Ram AFJ, et al.
Comparison of the Aspergillus niger genomic DNA sequence
with its genetic map. In: The Second Aspergillus Meeting. CA:
Asilomar Conference Center, 2005.
6 Semova N, Storms R, John T, et al. Generation, annotation, and
analysis of an extensive Aspergillus niger EST collection. BMC
Microbiol 2006; 6 : 7.
7 Perlman D, Kita DA, Peterson WA. Production of citric acid from
cane molasses. Arch Biochem 1946; 11 : 123 129.
8 Dai Z, Mao X, Magnuson J, Lasure L. Identification of genes
associated with morphology in Aspergillus niger by using suppres-
sion subtractive hybridization. Appl Env Micro 2004; 70 : 2474
2485.
9 Blom RH, Pfeifer VF, Moyer AJ, et al. Sodium gluconate
production fermentation with Aspergillus niger. Ind Eng Chem
1952; 44 : 435 440.
10 Moyer AJ, Umberger EJ, Stubbs JJ. Fermentation of concentrated
solutions of glucose to gluconic acid improved process. Ind Eng
Chem 1940; 32 : 1379 1383.
S20 Baker
Med Mycol Downloaded from informahealthcare by Marshall University on 05/23/
For personal use only.
11 Bos CJ, Debets AJ, Swart K, et al. Genetic analysis and the
construction of master strains for assignment of genes to six
linkage groups in Aspergillus niger. Curr Genet 1988; 14 : 437 443.
12 Debets F, Swart K, Hoekstra RF, Bos CJ. Genetic maps of eight
linkage groups of Aspergillus niger based on mitotic mapping.
Curr Genet 1993; 23 : 47 53.
13 Verdoes JC, Calil MR, Punt PJ, et al. The complete karyotype of
Aspergillus niger : the use of introduced electrophoretic mobility
variation of chromosomes for gene assignment studies. Mol Gen
Genet 1994; 244 : 75 80.
14 Debets AJ, Holub EF, Swart K, van den Broek HW, Bos CJ. An
electrophoretic karyotype of Aspergillus niger. Mol Gen Genet
1990; 224 : 264 268.
15 Swart K, Debets AJ, Bos CJ, et al. Genetic analysis in the
asexual fungus Aspergillus niger. Acta Biol Hung 2001; 52 : 335
343.
16 Galagan JE, Calvo SE, Cuomo C, et al. Sequencing of Aspergillus
nidulans and comparative analysis with A. fumigatus and A.
oryzae. Nature 2005; 438 (7071): 1105 1115.
17 Machida M, Asai K, Sano M, et al. Genome sequencing and
analysis of Aspergillus oryzae. Nature 2005; 438 (7071): 1157
1161.
18 Nierman WC, Pain A, Anderson MJ, et al. Genomic sequence of
the pathogenic and allergenic filamentous fungus Aspergillus
fumigatus. Nature 2005; 438 (7071): 1151 1156.
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Baker 2006 - Activity 1
Course: BS Nursing (BSN)
462 Documents
Students shared 462 documents in this course
Was this document helpful?
Aspergillus niger
genomics: Past, present and into the
future
SCOTT E. BAKER
Fungal Biotechnology Team, Pacific Northwest National Laboratory, Richland, Washington, USA
Aspergillus niger is a filamentous ascomycete fungus that is ubiquitous in the
environment and has been implicated in opportunistic infections of humans. In
addition to its role as an opportunistic human pathogen, A. niger is economically
important as a fermentation organism used for the production of citric acid.
Industrial citric acid production by A. niger represents one of the most efficient,
highest yield bioprocesses in use currently by industry. The genome size of A. niger
is estimated to be between 35.5 and 38.5 megabases (Mb) divided among
eight chromosomes/linkage groups that vary in size from 3.56.6 Mb. Currently,
there are three independent A. niger genome projects, an indication of the
economic importance of this organism. The rich amount of data resulting from
these multiple A. niger genome sequences will be used for basic and applied
research programs applicable to fermentation process development, morphology
and pathogenicity.
Keywords Aspergillus niger, genome, wildtype, mutant
Introduction
Aspergillus niger is a filamentous ascomycete fungus
that is ubiquitous in the environment and has been
implicated in opportunistic infections of humans [1].
A. niger is most widely known for its role as a citric
acid producer [2]. With production of citric acid at
over one million metric tons annually, A. niger citric
acid production serves as a model fungal fermentation
process. As a common member of the microbial
communities found in soils, A. niger plays a signifi-
cant role in the global carbon cycle. This organism is
a soil saprobe with a wide array of hydrolytic and
oxidative enzymes involved in the breakdown of plant
lignocellulose. A variety of these enzymes from A.
niger are important in the biotechnology industry. A.
niger is also an important model organism for several
important research areas including the study of
eukaryotic protein secretion in general, the effects
of various environmental factors on suppressing or
triggering the export of various biomass degrading
enzymes, molecular mechanisms critical to fermenta-
tion process development, and mechanisms involved
in the control of fungal morphology.
Currently, the genomes of three different strains of
A. niger have been sequenced (Table 1). Two of the
strains sequenced, NRRL 3 (ATCC 9029, CBS 120.49,
N400) and ATCC 1015 (NRRL 328, CBS 113.46) are
wildtype strains, while the other strain CBS 513.88, a
derivative of NRRL 3122 (ATCC 22343, CBS 115989)
was isolated after mutagenesis and selection for im-
proved glucoamylase production [S.W. Peterson, perso-
nal communication]. Most recently, in 2005, the
genome of A. niger ATCC 1015, a wildtype, historic
strain was used in research that resulted in the first
patented citric acid process [3], that was accepted for
sequencing through the US Department of Energy
(DOE) Microbial Genome Program (MGP). Organ-
isms accepted by this program are sequenced by
the DOE’s Joint Genome Institute (JGI). Another
wildtype A. niger strain, NRRL 3, was sequenced by
Integrated Genomics, a US based company. Finally,
CBS 513.88, a derivative of a mutant strain, NRRL
3122 was sequenced by a Netherlands based company,
DSM [4,5].
Correspondence: Scott E. Baker, Fungal Biotechnology Team, Pacific
Northwest National Laboratory, 902 Battelle Blvd., MSIN: K2-12,
Richland, Washington 99352, USA. Tel:
/1 509 372 4759. Fax: /1
509 372 4732. E-mail: scott.baker@pnl.gov
–2006 ISHAM DOI: 10.1080/13693780600921037
Medical Mycology
September 2006, 44, S17 S21
Med Mycol Downloaded from informahealthcare.com by Marshall University on 05/23/13
For personal use only.
